quorum 0.2.1 → 0.3.0
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- data/Gemfile.lock +35 -28
- data/HISTORY.md +4 -0
- data/app/assets/javascripts/quorum/application.js +1 -0
- data/app/assets/javascripts/quorum/jobs.js +5 -345
- data/app/assets/javascripts/quorum/quorum.js +275 -0
- data/app/assets/javascripts/quorum/template_settings.js +8 -0
- data/app/assets/javascripts/quorum/utilities.js +12 -0
- data/app/assets/stylesheets/quorum/application.css +0 -4
- data/app/assets/stylesheets/quorum/autohint.css +4 -0
- data/app/controllers/quorum/jobs_controller.rb +9 -9
- data/app/views/quorum/jobs/form/_blastn_form.html.erb +62 -62
- data/app/views/quorum/jobs/form/_blastp_form.html.erb +62 -62
- data/app/views/quorum/jobs/form/_blastx_form.html.erb +62 -62
- data/app/views/quorum/jobs/form/_tblastn_form.html.erb +62 -62
- data/app/views/quorum/jobs/show.html.erb +1 -1
- data/app/views/quorum/jobs/templates/_blast_detailed_report_template.html.erb +22 -22
- data/app/views/quorum/jobs/templates/_blast_template.html.erb +29 -29
- data/app/views/shared/_error_messages.html.erb +8 -8
- data/lib/quorum/version.rb +1 -1
- data/lib/tasks/jasmine.rake +8 -0
- data/quorum.gemspec +1 -0
- data/spec/data/seqs_not_fa.txt +16 -16
- data/spec/javascripts/fixtures/formatted_sequence.html +6 -0
- data/spec/javascripts/fixtures/quorum_search_form.html +461 -0
- data/spec/javascripts/fixtures/quorum_tabs.html +10 -0
- data/spec/javascripts/helpers/jasmine-jquery.js +288 -0
- data/spec/javascripts/jobs_spec.js +99 -0
- data/spec/javascripts/jquery/jquery-ui.min.js +791 -0
- data/spec/javascripts/jquery/jquery.min.js +4 -0
- data/spec/javascripts/jquery/jquery_ujs.js +373 -0
- data/spec/javascripts/quorum_spec.js +106 -0
- data/spec/javascripts/string_spec.js +18 -0
- data/spec/javascripts/support/jasmine.yml +84 -0
- data/spec/javascripts/support/jasmine_config.rb +23 -0
- data/spec/javascripts/support/jasmine_runner.rb +33 -0
- data/spec/requests/jobs_spec.rb +34 -33
- data/vendor/assets/javascripts/jquery.autohint.js +87 -0
- metadata +62 -26
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<form>
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<div>
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<textarea class="auto-hint" cols="40" id="job_sequence" name="job[sequence]" rows="20" title="Paste nucleic and amino acid FASTA sequence(s) here or upload a file below."></textarea>
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</div>
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<div>
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<input id="job_sequence_file" name="job[sequence_file]" type="file" />
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</div>
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<!-- Search Algorithms -->
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<!-- Comment out an algorithm below to remove it from the form. -->
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<!-- blastn -->
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<p>
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<strong>blastn</strong>
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<input name="job[blastn_job_attributes][queue]" type="hidden" value="0" /><input id="job_blastn_job_attributes_queue" name="job[blastn_job_attributes][queue]" type="checkbox" value="1" />
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</p>
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<div id="blastn" class="toggle">
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<table class="options">
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<tr>
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<td>
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<label>Database(s)</label>
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</td>
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<td>
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<select id="job_blastn_job_attributes_blast_dbs" multiple="multiple" name="job[blastn_job_attributes][blast_dbs][]"><option value="medp_acaau-20110120">Acacia aulacocarpa transcripts, build 20110120</option>
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<option value="medp_calan-20110119">Calophyllum antillanum transcripts, build 20110119</option>
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<option value="camptotheca_acuminata-20101112">Camptotheca acuminata transcripts, build 20101112</option>
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<option value="medp_cepha-20110617">Cephalotaxus harringtonia transcripts, build 20110617</option>
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<option value="medp_cinpu-20110618">Cinchona pubescens transcripts, build 20110618</option>
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<option value="colchicum_autumnale-20101112">Colchicum autumnale transcripts, build 20101112</option>
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<option value="medp_colfo-20110601">Coleus forskohlii transcripts, build 20110601</option>
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<option value="datura_ceratocaula-20101112">Datura ceratocaula transcripts, build 20101112</option>
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<option value="datura_innoxia-20101112">Datura innoxia transcripts, build 20101112</option>
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<option value="datura_me9-20101112">Datura metel transcripts, build 20101112</option>
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<option value="datura_stramonium-20100406">Datura stramonium transcripts, build 20100406</option>
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<option value="datura_stramonium-20101112">Datura stramonium transcripts, build 20101112</option>
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<option value="datura_wrightii-20101112">Datura wrightii transcripts, build 20101112</option>
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<option value="digitalis_lanata-20100406">Digitalis lanata transcripts, build 20100406</option>
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<option value="digitalis_lanata-20101112">Digitalis lanata transcripts, build 20101112</option>
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<option value="huperzia_lucidula-20101112">Huperzia lucidula transcripts, build 20101112</option>
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<option value="huperzia_squarrosa-20100406">Huperzia squarrosa transcripts, build 20100406</option>
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<option value="huperzia_squarrosa-20101112">Huperzia squarrosa transcripts, build 20101112</option>
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<option value="hyoscyamus_niger-20101112">Hyoscyamus niger transcripts, build 20101112</option>
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<option value="larrea_tridentata-20100406">Larrea tridentata transcripts, build 20100406</option>
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<option value="larrea_tridentata-20101112">Larrea tridentata transcripts, build 20101112</option>
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<option value="linum_flavum-20100207">Linum flavum transcripts, build 20100207</option>
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<option value="linum_flavum-20100406">Linum flavum transcripts, build 20100406</option>
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<option value="linum_flavum-20101112">Linum flavum transcripts, build 20101112</option>
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<option value="linum_usitatissimum-20101112">Linum usitatissimum transcripts, build 20101112</option>
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<option value="narcissus_9-20101112">Narcissus transcripts, build 20101112</option>
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<option value="papaver_somniferum-20100406">Papaver somniferum transcripts, build 20100406</option>
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<option value="papaver_somniferum-20101112">Papaver somniferum transcripts, build 20101112</option>
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<option value="medp_pilpe-20110620">Pilocarpus pennatifolius transcripts, build 20110620</option>
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<option value="podophyllum_hexandrum-20100406">Podophyllum hexandrum transcripts, build 20100406</option>
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<option value="podophyllum_hexandrum-20101112">Podophyllum hexandrum transcripts, build 20101112</option>
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<option value="podophyllum_peltatum-20101112">Podophyllum peltatum transcripts, build 20101112</option>
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<option value="taxus_x_media-20100126">Taxus x media transcripts, build 20100126</option>
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<option value="taxus_x_media-20100406">Taxus x media transcripts, build 20100406</option>
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<option value="taxus_x_media-20101112">Taxus x media transcripts, build 20101112</option>
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<option value="medp_trire-20110120">Tripterygium regelii transcripts, build 20110120</option></select>
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</td>
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<td>
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<label for="job_blastn_job_attributes_filter">DUST</label>
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</td>
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<td>
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<input name="job[blastn_job_attributes][filter]" type="hidden" value="0" /><input id="job_blastn_job_attributes_filter" name="job[blastn_job_attributes][filter]" type="checkbox" value="1" />
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</td>
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</tr>
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<tr>
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<td>
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<label for="job_blastn_job_attributes_expectation">Expectation</label>
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</td>
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<td>
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<input class="auto-hint" id="job_blastn_job_attributes_expectation" name="job[blastn_job_attributes][expectation]" size="15" title="5e-20" type="text" />
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</td>
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<td>
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<label for="job_blastn_job_attributes_min_bit_score">Min bit score</label>
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<td>
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<input class="auto-hint" id="job_blastn_job_attributes_min_bit_score" name="job[blastn_job_attributes][min_bit_score]" size="15" title="0" type="text" />
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<tr>
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<td>
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<label for="job_blastn_job_attributes_max_score">Max score</label>
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</td>
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<td>
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<input class="auto-hint" id="job_blastn_job_attributes_max_score" name="job[blastn_job_attributes][max_score]" size="15" title="25" type="text" />
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</td>
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<td>
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<label for="job_blastn_job_attributes_gapped_alignments">Gapped alignments</label>
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</td>
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<td>
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<select id="job_blastn_job_attributes_gapped_alignments" name="job[blastn_job_attributes][gapped_alignments]"><option value="false">No</option>
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<option value="true">Yes</option></select>
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</td>
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</tr>
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<tr>
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<td>
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<label for="job_blastn_job_attributes_gap_opening_extension">Gap opening extension</label>
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</td>
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<td>
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<select id="job_blastn_job_attributes_gap_opening_extension" name="job[blastn_job_attributes][gap_opening_extension]"><option value="">--Select--</option>
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<option value="32767,32767">32767, 32767</option>
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<option value="11,2">11, 2</option>
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<option value="10,2">10, 2</option>
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<option value="9,2">9, 2</option>
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<option value="8,2">8, 2</option>
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<option value="7,2">7, 2</option>
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<option value="6,2">6, 2</option>
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<option value="13,1">13, 1</option>
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<option value="12,1">12, 1</option>
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<option value="11,1">11, 1</option>
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<option value="10,1">10, 1</option>
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<option value="9,1">9, 1</option></select>
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</td>
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<td></td>
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<td></td>
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</tr>
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</table>
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</div>
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<!-- blastx -->
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<p>
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<strong>blastx</strong>
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<input name="job[blastx_job_attributes][queue]" type="hidden" value="0" /><input id="job_blastx_job_attributes_queue" name="job[blastx_job_attributes][queue]" type="checkbox" value="1" />
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</p>
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<div id="blastx" class="toggle">
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<table class="options">
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<tr>
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<td>
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<label>Database(s)</label>
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</td>
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<td>
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<select id="job_blastx_job_attributes_blast_dbs" multiple="multiple" name="job[blastx_job_attributes][blast_dbs][]"><option value="medp_acaau-20110120">Acacia aulacocarpa peptides, build 20110120</option>
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<option value="medp_calan-20110119">Calophyllum antillanum peptides, build 20110119</option>
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<option value="camptotheca_acuminata-20101112">Camptotheca acuminata peptides, build 20101112</option>
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<option value="medp_cepha-20110617">Cephalotaxus harringtonia peptides, build 20110617</option>
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<option value="medp_cinpu-20110618">Cinchona pubescens peptides, build 20110618</option>
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<option value="colchicum_autumnale-20101112">Colchicum autumnale peptides, build 20101112</option>
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<option value="medp_colfo-20110601">Coleus forskohlii peptides, build 20110601</option>
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<option value="datura_ceratocaula-20101112">Datura ceratocaula peptides, build 20101112</option>
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<option value="datura_innoxia-20101112">Datura innoxia peptides transcripts, build 20101112</option>
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<option value="datura_me9-20101112">Datura metel peptides, build 20101112</option>
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<option value="datura_stramonium-20100406">Datura stramonium peptides, build 20100406</option>
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<option value="datura_stramonium-20101112">Datura stramonium peptides, build 20101112</option>
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<option value="datura_wrightii-20101112">Datura wrightii peptides, build 20101112</option>
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<option value="digitalis_lanata-20100406">Digitalis lanata peptides, build 20100406</option>
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<option value="digitalis_lanata-20101112">Digitalis lanata peptides, build 20101112</option>
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<option value="huperzia_lucidula-20101112">Huperzia lucidula peptides, build 20101112</option>
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<option value="huperzia_squarrosa-20100406">Huperzia squarrosa peptides, build 20100406</option>
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<option value="huperzia_squarrosa-20101112">Huperzia squarrosa peptides, build 20101112</option>
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<option value="hyoscyamus_niger-20101112">Hyoscyamus niger peptides, build 20101112</option>
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<option value="larrea_tridentata-20100406">Larrea tridentata peptides, build 20100406</option>
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<option value="larrea_tridentata-20101112">Larrea tridentata peptides, build 20101112</option>
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<option value="linum_flavum-20100406">Linum flavum peptides, build 20100406</option>
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<option value="linum_flavum-20101112">Linum flavum peptides, build 20101112</option>
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<option value="linum_usitatissimum-20101112">Linum usitatissimum peptides, build 20101112</option>
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<option value="narcissus_9-20101112">Narcissus peptides, build 20101112</option>
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<option value="papaver_somniferum-20100406">Papaver somniferum peptides, build 20100406</option>
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<option value="papaver_somniferum-20101112">Papaver somniferum peptides, build 20101112</option>
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<option value="medp_pilpe-20110620">Pilocarpus pennatifolius peptides, build 20110620</option>
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<option value="podophyllum_hexandrum-20100406">Podophyllum hexandrum peptides, build 20100406</option>
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<option value="podophyllum_hexandrum-20101112">Podophyllum hexandrum peptides, build 20101112</option>
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<option value="podophyllum_peltatum-20101112">Podophyllum peltatum peptides, build 20101112</option>
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<option value="taxus_x_media-20100406">Taxus x media peptides, build 20100406</option>
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<option value="taxus_x_media-20101112">Taxus x media peptides, build 20101112</option>
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<option value="medp_trire-20110120">Tripterygium regelii peptides, build 20110120</option></select>
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</td>
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<td>
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<label for="job_blastx_job_attributes_filter">SEG</label>
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</td>
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<td>
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<input name="job[blastx_job_attributes][filter]" type="hidden" value="0" /><input id="job_blastx_job_attributes_filter" name="job[blastx_job_attributes][filter]" type="checkbox" value="1" />
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</td>
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</tr>
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<tr>
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<td>
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<label for="job_blastx_job_attributes_expectation">Expectation</label>
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</td>
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<td>
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184
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<input class="auto-hint" id="job_blastx_job_attributes_expectation" name="job[blastx_job_attributes][expectation]" size="15" title="5e-20" type="text" />
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</td>
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<td>
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<label for="job_blastx_job_attributes_min_bit_score">Min bit score</label>
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</td>
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189
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<td>
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190
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<input class="auto-hint" id="job_blastx_job_attributes_min_bit_score" name="job[blastx_job_attributes][min_bit_score]" size="15" title="0" type="text" />
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</td>
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</tr>
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<tr>
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<td>
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<label for="job_blastx_job_attributes_max_score">Max score</label>
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</td>
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<td>
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198
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<input class="auto-hint" id="job_blastx_job_attributes_max_score" name="job[blastx_job_attributes][max_score]" size="15" title="25" type="text" />
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</td>
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<td>
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<label for="job_blastx_job_attributes_gapped_alignments">Gapped alignments</label>
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</td>
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<td>
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<select id="job_blastx_job_attributes_gapped_alignments" name="job[blastx_job_attributes][gapped_alignments]"><option value="false">No</option>
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<option value="true">Yes</option></select>
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</td>
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</tr>
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<tr>
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<td>
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<label for="job_blastx_job_attributes_gap_opening_extension">Gap opening extension</label>
|
|
211
|
+
</td>
|
|
212
|
+
<td>
|
|
213
|
+
<select id="job_blastx_job_attributes_gap_opening_extension" name="job[blastx_job_attributes][gap_opening_extension]"><option value="">--Select--</option>
|
|
214
|
+
<option value="32767,32767">32767, 32767</option>
|
|
215
|
+
<option value="11,2">11, 2</option>
|
|
216
|
+
<option value="10,2">10, 2</option>
|
|
217
|
+
<option value="9,2">9, 2</option>
|
|
218
|
+
<option value="8,2">8, 2</option>
|
|
219
|
+
<option value="7,2">7, 2</option>
|
|
220
|
+
<option value="6,2">6, 2</option>
|
|
221
|
+
<option value="13,1">13, 1</option>
|
|
222
|
+
<option value="12,1">12, 1</option>
|
|
223
|
+
<option value="11,1">11, 1</option>
|
|
224
|
+
<option value="10,1">10, 1</option>
|
|
225
|
+
<option value="9,1">9, 1</option></select>
|
|
226
|
+
</td>
|
|
227
|
+
<td></td>
|
|
228
|
+
<td></td>
|
|
229
|
+
</tr>
|
|
230
|
+
</table>
|
|
231
|
+
</div>
|
|
232
|
+
|
|
233
|
+
|
|
234
|
+
<!-- tblastn -->
|
|
235
|
+
|
|
236
|
+
<p>
|
|
237
|
+
<strong>tblastn</strong>
|
|
238
|
+
<input name="job[tblastn_job_attributes][queue]" type="hidden" value="0" /><input id="job_tblastn_job_attributes_queue" name="job[tblastn_job_attributes][queue]" type="checkbox" value="1" />
|
|
239
|
+
</p>
|
|
240
|
+
<div id="tblastn" class="toggle">
|
|
241
|
+
<table class="options">
|
|
242
|
+
<tr>
|
|
243
|
+
<td>
|
|
244
|
+
<label>Database(s)</label>
|
|
245
|
+
</td>
|
|
246
|
+
<td>
|
|
247
|
+
<select id="job_tblastn_job_attributes_blast_dbs" multiple="multiple" name="job[tblastn_job_attributes][blast_dbs][]"><option value="medp_acaau-20110120">Acacia aulacocarpa transcripts, build 20110120</option>
|
|
248
|
+
<option value="medp_calan-20110119">Calophyllum antillanum transcripts, build 20110119</option>
|
|
249
|
+
<option value="camptotheca_acuminata-20101112">Camptotheca acuminata transcripts, build 20101112</option>
|
|
250
|
+
<option value="medp_cepha-20110617">Cephalotaxus harringtonia transcripts, build 20110617</option>
|
|
251
|
+
<option value="medp_cinpu-20110618">Cinchona pubescens transcripts, build 20110618</option>
|
|
252
|
+
<option value="colchicum_autumnale-20101112">Colchicum autumnale transcripts, build 20101112</option>
|
|
253
|
+
<option value="medp_colfo-20110601">Coleus forskohlii transcripts, build 20110601</option>
|
|
254
|
+
<option value="datura_ceratocaula-20101112">Datura ceratocaula transcripts, build 20101112</option>
|
|
255
|
+
<option value="datura_innoxia-20101112">Datura innoxia transcripts, build 20101112</option>
|
|
256
|
+
<option value="datura_me9-20101112">Datura metel transcripts, build 20101112</option>
|
|
257
|
+
<option value="datura_stramonium-20100406">Datura stramonium transcripts, build 20100406</option>
|
|
258
|
+
<option value="datura_stramonium-20101112">Datura stramonium transcripts, build 20101112</option>
|
|
259
|
+
<option value="datura_wrightii-20101112">Datura wrightii transcripts, build 20101112</option>
|
|
260
|
+
<option value="digitalis_lanata-20100406">Digitalis lanata transcripts, build 20100406</option>
|
|
261
|
+
<option value="digitalis_lanata-20101112">Digitalis lanata transcripts, build 20101112</option>
|
|
262
|
+
<option value="huperzia_lucidula-20101112">Huperzia lucidula transcripts, build 20101112</option>
|
|
263
|
+
<option value="huperzia_squarrosa-20100406">Huperzia squarrosa transcripts, build 20100406</option>
|
|
264
|
+
<option value="huperzia_squarrosa-20101112">Huperzia squarrosa transcripts, build 20101112</option>
|
|
265
|
+
<option value="hyoscyamus_niger-20101112">Hyoscyamus niger transcripts, build 20101112</option>
|
|
266
|
+
<option value="larrea_tridentata-20100406">Larrea tridentata transcripts, build 20100406</option>
|
|
267
|
+
<option value="larrea_tridentata-20101112">Larrea tridentata transcripts, build 20101112</option>
|
|
268
|
+
<option value="linum_flavum-20100207">Linum flavum transcripts, build 20100207</option>
|
|
269
|
+
<option value="linum_flavum-20100406">Linum flavum transcripts, build 20100406</option>
|
|
270
|
+
<option value="linum_flavum-20101112">Linum flavum transcripts, build 20101112</option>
|
|
271
|
+
<option value="linum_usitatissimum-20101112">Linum usitatissimum transcripts, build 20101112</option>
|
|
272
|
+
<option value="narcissus_9-20101112">Narcissus transcripts, build 20101112</option>
|
|
273
|
+
<option value="papaver_somniferum-20100406">Papaver somniferum transcripts, build 20100406</option>
|
|
274
|
+
<option value="papaver_somniferum-20101112">Papaver somniferum transcripts, build 20101112</option>
|
|
275
|
+
<option value="medp_pilpe-20110620">Pilocarpus pennatifolius transcripts, build 20110620</option>
|
|
276
|
+
<option value="podophyllum_hexandrum-20100406">Podophyllum hexandrum transcripts, build 20100406</option>
|
|
277
|
+
<option value="podophyllum_hexandrum-20101112">Podophyllum hexandrum transcripts, build 20101112</option>
|
|
278
|
+
<option value="podophyllum_peltatum-20101112">Podophyllum peltatum transcripts, build 20101112</option>
|
|
279
|
+
<option value="taxus_x_media-20100126">Taxus x media transcripts, build 20100126</option>
|
|
280
|
+
<option value="taxus_x_media-20100406">Taxus x media transcripts, build 20100406</option>
|
|
281
|
+
<option value="taxus_x_media-20101112">Taxus x media transcripts, build 20101112</option>
|
|
282
|
+
<option value="medp_trire-20110120">Tripterygium regelii transcripts, build 20110120</option></select>
|
|
283
|
+
</td>
|
|
284
|
+
<td>
|
|
285
|
+
<label for="job_tblastn_job_attributes_filter">SEG</label>
|
|
286
|
+
</td>
|
|
287
|
+
<td>
|
|
288
|
+
<input name="job[tblastn_job_attributes][filter]" type="hidden" value="0" /><input id="job_tblastn_job_attributes_filter" name="job[tblastn_job_attributes][filter]" type="checkbox" value="1" />
|
|
289
|
+
</td>
|
|
290
|
+
</tr>
|
|
291
|
+
<tr>
|
|
292
|
+
<td>
|
|
293
|
+
<label for="job_tblastn_job_attributes_expectation">Expectation</label>
|
|
294
|
+
</td>
|
|
295
|
+
<td>
|
|
296
|
+
<input class="auto-hint" id="job_tblastn_job_attributes_expectation" name="job[tblastn_job_attributes][expectation]" size="15" title="5e-20" type="text" />
|
|
297
|
+
</td>
|
|
298
|
+
<td>
|
|
299
|
+
<label for="job_tblastn_job_attributes_min_bit_score">Min bit score</label>
|
|
300
|
+
</td>
|
|
301
|
+
<td>
|
|
302
|
+
<input class="auto-hint" id="job_tblastn_job_attributes_min_bit_score" name="job[tblastn_job_attributes][min_bit_score]" size="15" title="0" type="text" />
|
|
303
|
+
</td>
|
|
304
|
+
</tr>
|
|
305
|
+
<tr>
|
|
306
|
+
<td>
|
|
307
|
+
<label for="job_tblastn_job_attributes_max_score">Max score</label>
|
|
308
|
+
</td>
|
|
309
|
+
<td>
|
|
310
|
+
<input class="auto-hint" id="job_tblastn_job_attributes_max_score" name="job[tblastn_job_attributes][max_score]" size="15" title="25" type="text" />
|
|
311
|
+
</td>
|
|
312
|
+
<td>
|
|
313
|
+
<label for="job_tblastn_job_attributes_gapped_alignments">Gapped alignments</label>
|
|
314
|
+
</td>
|
|
315
|
+
<td>
|
|
316
|
+
<select id="job_tblastn_job_attributes_gapped_alignments" name="job[tblastn_job_attributes][gapped_alignments]"><option value="false">No</option>
|
|
317
|
+
<option value="true">Yes</option></select>
|
|
318
|
+
</td>
|
|
319
|
+
</tr>
|
|
320
|
+
<tr>
|
|
321
|
+
<td>
|
|
322
|
+
<label for="job_tblastn_job_attributes_gap_opening_extension">Gap opening extension</label>
|
|
323
|
+
</td>
|
|
324
|
+
<td>
|
|
325
|
+
<select id="job_tblastn_job_attributes_gap_opening_extension" name="job[tblastn_job_attributes][gap_opening_extension]"><option value="">--Select--</option>
|
|
326
|
+
<option value="32767,32767">32767, 32767</option>
|
|
327
|
+
<option value="11,2">11, 2</option>
|
|
328
|
+
<option value="10,2">10, 2</option>
|
|
329
|
+
<option value="9,2">9, 2</option>
|
|
330
|
+
<option value="8,2">8, 2</option>
|
|
331
|
+
<option value="7,2">7, 2</option>
|
|
332
|
+
<option value="6,2">6, 2</option>
|
|
333
|
+
<option value="13,1">13, 1</option>
|
|
334
|
+
<option value="12,1">12, 1</option>
|
|
335
|
+
<option value="11,1">11, 1</option>
|
|
336
|
+
<option value="10,1">10, 1</option>
|
|
337
|
+
<option value="9,1">9, 1</option></select>
|
|
338
|
+
</td>
|
|
339
|
+
<td></td>
|
|
340
|
+
<td></td>
|
|
341
|
+
</tr>
|
|
342
|
+
</table>
|
|
343
|
+
</div>
|
|
344
|
+
|
|
345
|
+
|
|
346
|
+
<!-- blastp -->
|
|
347
|
+
|
|
348
|
+
<p>
|
|
349
|
+
<strong>blastp</strong>
|
|
350
|
+
<input name="job[blastp_job_attributes][queue]" type="hidden" value="0" /><input id="job_blastp_job_attributes_queue" name="job[blastp_job_attributes][queue]" type="checkbox" value="1" />
|
|
351
|
+
</p>
|
|
352
|
+
<div id="blastp" class="toggle">
|
|
353
|
+
<table class="options">
|
|
354
|
+
<tr>
|
|
355
|
+
<td>
|
|
356
|
+
<label>Database(s)</label>
|
|
357
|
+
</td>
|
|
358
|
+
<td>
|
|
359
|
+
<select id="job_blastp_job_attributes_blast_dbs" multiple="multiple" name="job[blastp_job_attributes][blast_dbs][]"><option value="medp_acaau-20110120">Acacia aulacocarpa peptides, build 20110120</option>
|
|
360
|
+
<option value="medp_calan-20110119">Calophyllum antillanum peptides, build 20110119</option>
|
|
361
|
+
<option value="camptotheca_acuminata-20101112">Camptotheca acuminata peptides, build 20101112</option>
|
|
362
|
+
<option value="medp_cepha-20110617">Cephalotaxus harringtonia peptides, build 20110617</option>
|
|
363
|
+
<option value="medp_cinpu-20110618">Cinchona pubescens peptides, build 20110618</option>
|
|
364
|
+
<option value="colchicum_autumnale-20101112">Colchicum autumnale peptides, build 20101112</option>
|
|
365
|
+
<option value="medp_colfo-20110601">Coleus forskohlii peptides, build 20110601</option>
|
|
366
|
+
<option value="datura_ceratocaula-20101112">Datura ceratocaula peptides, build 20101112</option>
|
|
367
|
+
<option value="datura_innoxia-20101112">Datura innoxia peptides, build 20101112</option>
|
|
368
|
+
<option value="datura_me9-20101112">Datura metel peptides, build 20101112</option>
|
|
369
|
+
<option value="datura_stramonium-20100406">Datura stramonium peptides, build 20100406</option>
|
|
370
|
+
<option value="datura_stramonium-20101112">Datura stramonium peptides, build 20101112</option>
|
|
371
|
+
<option value="datura_wrightii-20101112">Datura wrightii peptides, build 20101112</option>
|
|
372
|
+
<option value="digitalis_lanata-20100406">Digitalis lanata peptides, build 20100406</option>
|
|
373
|
+
<option value="digitalis_lanata-20101112">Digitalis lanata peptides, build 20101112</option>
|
|
374
|
+
<option value="huperzia_lucidula-20101112">Huperzia lucidula peptides, build 20101112</option>
|
|
375
|
+
<option value="huperzia_squarrosa-20100406">Huperzia squarrosa peptides, build 20100406</option>
|
|
376
|
+
<option value="huperzia_squarrosa-20101112">Huperzia squarrosa peptides, build 20101112</option>
|
|
377
|
+
<option value="hyoscyamus_niger-20101112">Hyoscyamus niger peptides, build 20101112</option>
|
|
378
|
+
<option value="larrea_tridentata-20100406">Larrea tridentata peptides, build 20100406</option>
|
|
379
|
+
<option value="larrea_tridentata-20101112">Larrea tridentata peptides, build 20101112</option>
|
|
380
|
+
<option value="linum_flavum-20100406">Linum flavum peptides, build 20100406</option>
|
|
381
|
+
<option value="linum_flavum-20101112">Linum flavum peptides, build 20101112</option>
|
|
382
|
+
<option value="linum_usitatissimum-20101112">Linum usitatissimum peptides, build 20101112</option>
|
|
383
|
+
<option value="narcissus_9-20101112">Narcissus peptides, build 20101112</option>
|
|
384
|
+
<option value="papaver_somniferum-20100406">Papaver somniferum peptides, build 20100406</option>
|
|
385
|
+
<option value="papaver_somniferum-20101112">Papaver somniferum peptides, build 20101112</option>
|
|
386
|
+
<option value="medp_pilpe-20110620">Pilocarpus pennatifolius peptides, build 20110620</option>
|
|
387
|
+
<option value="podophyllum_hexandrum-20100406">Podophyllum hexandrum peptides, build 20100406</option>
|
|
388
|
+
<option value="podophyllum_hexandrum-20101112">Podophyllum hexandrum peptides, build 20101112</option>
|
|
389
|
+
<option value="podophyllum_peltatum-20101112">Podophyllum peltatum peptides, build 20101112</option>
|
|
390
|
+
<option value="taxus_x_media-20100406">Taxus x media peptides, build 20100406</option>
|
|
391
|
+
<option value="taxus_x_media-20101112">Taxus x media peptides, build 20101112</option>
|
|
392
|
+
<option value="medp_trire-20110120">Tripterygium regelii peptides, build 20110120</option></select>
|
|
393
|
+
</td>
|
|
394
|
+
<td>
|
|
395
|
+
<label for="job_blastp_job_attributes_filter">SEG</label>
|
|
396
|
+
</td>
|
|
397
|
+
<td>
|
|
398
|
+
<input name="job[blastp_job_attributes][filter]" type="hidden" value="0" /><input id="job_blastp_job_attributes_filter" name="job[blastp_job_attributes][filter]" type="checkbox" value="1" />
|
|
399
|
+
</td>
|
|
400
|
+
</tr>
|
|
401
|
+
<tr>
|
|
402
|
+
<td>
|
|
403
|
+
<label for="job_blastp_job_attributes_expectation">Expectation</label>
|
|
404
|
+
</td>
|
|
405
|
+
<td>
|
|
406
|
+
<input class="auto-hint" id="job_blastp_job_attributes_expectation" name="job[blastp_job_attributes][expectation]" size="15" title="5e-20" type="text" />
|
|
407
|
+
</td>
|
|
408
|
+
<td>
|
|
409
|
+
<label for="job_blastp_job_attributes_min_bit_score">Min bit score</label>
|
|
410
|
+
</td>
|
|
411
|
+
<td>
|
|
412
|
+
<input class="auto-hint" id="job_blastp_job_attributes_min_bit_score" name="job[blastp_job_attributes][min_bit_score]" size="15" title="0" type="text" />
|
|
413
|
+
</td>
|
|
414
|
+
</tr>
|
|
415
|
+
<tr>
|
|
416
|
+
<td>
|
|
417
|
+
<label for="job_blastp_job_attributes_max_score">Max score</label>
|
|
418
|
+
</td>
|
|
419
|
+
<td>
|
|
420
|
+
<input class="auto-hint" id="job_blastp_job_attributes_max_score" name="job[blastp_job_attributes][max_score]" size="15" title="25" type="text" />
|
|
421
|
+
</td>
|
|
422
|
+
<td>
|
|
423
|
+
<label for="job_blastp_job_attributes_gapped_alignments">Gapped alignments</label>
|
|
424
|
+
</td>
|
|
425
|
+
<td>
|
|
426
|
+
<select id="job_blastp_job_attributes_gapped_alignments" name="job[blastp_job_attributes][gapped_alignments]"><option value="false">No</option>
|
|
427
|
+
<option value="true">Yes</option></select>
|
|
428
|
+
</td>
|
|
429
|
+
</tr>
|
|
430
|
+
<tr>
|
|
431
|
+
<td>
|
|
432
|
+
<label for="job_blastp_job_attributes_gap_opening_extension">Gap opening extension</label>
|
|
433
|
+
</td>
|
|
434
|
+
<td>
|
|
435
|
+
<select id="job_blastp_job_attributes_gap_opening_extension" name="job[blastp_job_attributes][gap_opening_extension]"><option value="">--Select--</option>
|
|
436
|
+
<option value="32767,32767">32767, 32767</option>
|
|
437
|
+
<option value="11,2">11, 2</option>
|
|
438
|
+
<option value="10,2">10, 2</option>
|
|
439
|
+
<option value="9,2">9, 2</option>
|
|
440
|
+
<option value="8,2">8, 2</option>
|
|
441
|
+
<option value="7,2">7, 2</option>
|
|
442
|
+
<option value="6,2">6, 2</option>
|
|
443
|
+
<option value="13,1">13, 1</option>
|
|
444
|
+
<option value="12,1">12, 1</option>
|
|
445
|
+
<option value="11,1">11, 1</option>
|
|
446
|
+
<option value="10,1">10, 1</option>
|
|
447
|
+
<option value="9,1">9, 1</option></select>
|
|
448
|
+
</td>
|
|
449
|
+
<td></td>
|
|
450
|
+
<td></td>
|
|
451
|
+
</tr>
|
|
452
|
+
</table>
|
|
453
|
+
</div>
|
|
454
|
+
|
|
455
|
+
|
|
456
|
+
<!-- End Search Algorithms -->
|
|
457
|
+
<div>
|
|
458
|
+
<input name="commit" type="submit" value="Submit" />
|
|
459
|
+
<input id="quorum_job_reset" name="reset" type="button" value="Reset" />
|
|
460
|
+
</div>
|
|
461
|
+
</form>
|