sequenceserver 3.0.1 → 3.1.1

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Files changed (62) hide show
  1. checksums.yaml +4 -4
  2. data/bin/sequenceserver +2 -2
  3. data/lib/sequenceserver/api_errors.rb +32 -2
  4. data/lib/sequenceserver/blast/job.rb +20 -3
  5. data/lib/sequenceserver/blast/report.rb +74 -86
  6. data/lib/sequenceserver/blast/tasks.rb +38 -0
  7. data/lib/sequenceserver/config.rb +54 -20
  8. data/lib/sequenceserver/makeblastdb.rb +16 -2
  9. data/lib/sequenceserver/report.rb +0 -6
  10. data/lib/sequenceserver/routes.rb +66 -25
  11. data/lib/sequenceserver/sequence.rb +35 -7
  12. data/lib/sequenceserver/server.rb +1 -1
  13. data/lib/sequenceserver/version.rb +1 -1
  14. data/lib/sequenceserver.rb +1 -1
  15. data/public/404.html +1 -1
  16. data/public/css/app.css +121 -0
  17. data/public/css/app.min.css +1 -0
  18. data/public/css/sequenceserver.css +0 -148
  19. data/public/css/sequenceserver.min.css +3 -3
  20. data/public/js/circos.js +2 -2
  21. data/public/js/collapse_preferences.js +37 -0
  22. data/public/js/databases.js +65 -37
  23. data/public/js/databases_tree.js +2 -1
  24. data/public/js/dnd.js +37 -50
  25. data/public/js/download_fasta.js +1 -0
  26. data/public/js/form.js +79 -50
  27. data/public/js/grapher.js +23 -37
  28. data/public/js/hits_overview.js +2 -2
  29. data/public/js/kablammo.js +2 -2
  30. data/public/js/length_distribution.js +3 -3
  31. data/public/js/null_plugins/grapher/histogram.js +25 -0
  32. data/public/js/null_plugins/options.js +3 -0
  33. data/public/js/null_plugins/query_stats.js +11 -0
  34. data/public/js/null_plugins/report_plugins.js +6 -1
  35. data/public/js/null_plugins/search_header_plugin.js +4 -0
  36. data/public/js/options.js +161 -56
  37. data/public/js/query.js +85 -59
  38. data/public/js/report.js +1 -1
  39. data/public/js/search.js +2 -0
  40. data/public/js/search_button.js +67 -56
  41. data/public/js/sidebar.js +10 -1
  42. data/public/js/tests/database.spec.js +5 -5
  43. data/public/js/tests/form.spec.js +98 -0
  44. data/public/js/tests/mock_data/databases.json +5 -5
  45. data/public/js/tests/mocks/circos.js +6 -0
  46. data/public/js/tests/report.spec.js +4 -3
  47. data/public/js/tests/search_query.spec.js +16 -6
  48. data/public/sequenceserver-report.min.js +46 -24
  49. data/public/sequenceserver-search.min.js +57 -13
  50. data/public/sequenceserver_logo.webp +0 -0
  51. data/views/blastn_options.erb +66 -66
  52. data/views/blastp_options.erb +59 -59
  53. data/views/blastx_options.erb +68 -68
  54. data/views/layout.erb +61 -3
  55. data/views/search.erb +33 -38
  56. data/views/search_layout.erb +153 -0
  57. data/views/tblastn_options.erb +57 -57
  58. data/views/tblastx_options.erb +64 -64
  59. metadata +51 -22
  60. data/lib/sequenceserver/makeblastdb-modified-with-cache.rb +0 -345
  61. data/public/SequenceServer_logo.png +0 -0
  62. data/public/js/tests/advanced_parameters.spec.js +0 -36
data/views/blastp_options.erb CHANGED
@@ -4,40 +4,40 @@
4
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  characters per line to preserve formatting.
5
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  %>
6
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- <h5>General Search Options</h5>
8
- <ul class="list-unstyled">
7
+ <h5 class="text-lg py-4 font-medium">General Search Options</h5>
8
+ <ul class="list-unstyled space-y-2">
9
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  <li>
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- <pre><%= ERB::Util.h %q|-task <String, Permissible values: 'blastp' 'blastp-fast' 'blastp-short'>
10
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-task <String, Permissible values: 'blastp' 'blastp-fast' 'blastp-short'>
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  Task to execute
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  Default = 'blastp'|%></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-evalue <Real>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-evalue <Real>
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  Expectation value (E) threshold for saving hits
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  Default = '10'| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-word_size <Integer, >=2>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-word_size <Integer, >=2>
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  Word size for wordfinder algorithm| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-gapopen <Integer>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-gapopen <Integer>
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  Cost to open a gap| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-gapextend <Integer>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-gapextend <Integer>
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  Cost to extend a gap| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-matrix <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-matrix <String>
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  Scoring matrix name (normally BLOSUM62)| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-threshold <Real, >=0>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-threshold <Real, >=0>
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  Minimum word score such that the word is added to the BLAST lookup table| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-comp_based_stats <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-comp_based_stats <String>
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  Use composition-based statistics:
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  D or d: default (equivalent to 2)
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  0 or F or f: no composition-based statistics
@@ -52,23 +52,23 @@
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  </ul>
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  <br />
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- <h5>Formatting Options</h5>
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- <ul class="list-unstyled">
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+ <h5 class="text-lg py-4 font-medium">Formatting Options</h5>
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+ <ul class="list-unstyled space-y-2">
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  <li>
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- <pre><%= ERB::Util.h %q|-num_descriptions <Integer, >=0>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-num_descriptions <Integer, >=0>
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  Number of database sequences to show one-line descriptions for
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  Not applicable for outfmt > 4
61
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  Default = '500'
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  * Incompatible with: max_target_seqs| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q| -num_alignments <Integer, >=0>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q| -num_alignments <Integer, >=0>
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  Number of database sequences to show alignments for
67
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  Default = '250'
68
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  * Incompatible with: max_target_seqs| %></pre>
69
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q| -sorthits <Integer, (>=0 and =<4)>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q| -sorthits <Integer, (>=0 and =<4)>
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  Sorting option for hits:
73
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  alignment view options:
74
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  0 = Sort by evalue,
@@ -79,7 +79,7 @@
79
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  Not applicable for outfmt > 4| %></pre>
80
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  </li>
81
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  <li>
82
- <pre><%= ERB::Util.h %q| -sorthsps <Integer, (>=0 and =<4)>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q| -sorthsps <Integer, (>=0 and =<4)>
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  Sorting option for hps:
84
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  0 = Sort by hsp evalue,
85
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  1 = Sort by hsp score,
@@ -92,52 +92,52 @@
92
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93
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  <br/>
94
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95
- <h5>Query filtering options</h5>
96
- <ul class="list-unstyled">
95
+ <h5 class="text-lg py-4 font-medium">Query filtering options</h5>
96
+ <ul class="list-unstyled space-y-2">
97
97
  <li>
98
- <pre><%= ERB::Util.h %q|-seg <String>
98
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-seg <String>
99
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  Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
100
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  or 'no' to disable)
101
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  Default = 'no'| %></pre>
102
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  </li>
103
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  <li>
104
- <pre><%= ERB::Util.h %q|-soft_masking <Boolean>
104
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-soft_masking <Boolean>
105
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  Apply filtering locations as soft masks
106
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  Default = 'false'| %></pre>
107
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  </li>
108
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  <li>
109
- <pre><%= ERB::Util.h %q|-lcase_masking
109
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-lcase_masking
110
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  Use lower case filtering in query and subject sequence(s)?| %></pre>
111
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  </li>
112
112
  </ul>
113
113
 
114
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  <br/>
115
115
 
116
- <h5>Restrict search or results</h5>
117
- <ul class="list-unstyled">
116
+ <h5 class="text-lg py-4 font-medium">Restrict search or results</h5>
117
+ <ul class="list-unstyled space-y-2">
118
118
  <li>
119
- <pre><%= ERB::Util.h %q|-gilist <String>
119
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-gilist <String>
120
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  Restrict search of database to list of GIs
121
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  * Incompatible with: seqidlist, taxids, taxidlist, negative_gilist,
122
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  negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
123
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  subject_loc| %></pre>
124
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  </li>
125
125
  <li>
126
- <pre><%= ERB::Util.h %q|-seqidlist <String>
126
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-seqidlist <String>
127
127
  Restrict search of database to list of SeqIDs
128
128
  * Incompatible with: gilist, taxids, taxidlist, negative_gilist,
129
129
  negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
130
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  subject_loc| %></pre>
131
131
  </li>
132
132
  <li>
133
- <pre><%= ERB::Util.h %q|-negative_gilist <String>
133
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-negative_gilist <String>
134
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  Restrict search of database to everything except the specified GIs
135
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  * Incompatible with: gilist, seqidlist, taxids, taxidlist,
136
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  negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
137
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  subject_loc| %></pre>
138
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  </li>
139
139
  <li>
140
- <pre><%= ERB::Util.h %q|-negative_seqidlist <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-negative_seqidlist <String>
141
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  Restrict search of database to everything except the specified SeqIDs
142
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  * Incompatible with: gilist, seqidlist, taxids, taxidlist,
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  negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
@@ -145,88 +145,88 @@
145
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  </li>
146
146
  <li>
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147
  <li>
148
- <pre><%= ERB::Util.h %q|-taxids <String>
148
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-taxids <String>
149
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  Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')
150
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  * Incompatible with: gilist, seqidlist, taxidlist, negative_gilist,
151
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  negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
152
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  subject_loc| %></pre>
153
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  </li>
154
154
  <li>
155
- <pre><%= ERB::Util.h %q|-negative_taxids <String>
155
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-negative_taxids <String>
156
156
  Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')
157
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  * Incompatible with: gilist, seqidlist, taxids, taxidlist,
158
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  negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
159
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  subject_loc| %></pre>
160
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  </li>
161
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  <li>
162
- <pre><%= ERB::Util.h %q|-taxidlist <String>
162
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-taxidlist <String>
163
163
  Restrict search of database to include only the specified taxonomy IDs
164
164
  * Incompatible with: gilist, seqidlist, taxids, negative_gilist,
165
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  negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
166
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  subject_loc| %></pre>
167
167
  </li>
168
168
  <li>
169
- <pre><%= ERB::Util.h %q|-negative_taxidlist <String>
169
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-negative_taxidlist <String>
170
170
  Restrict search of database to everything except the specified taxonomy IDs
171
171
  * Incompatible with: gilist, seqidlist, taxids, taxidlist,
172
172
  negative_gilist, negative_seqidlist, negative_taxids, remote, subject,
173
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  subject_loc| %></pre>
174
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  </li>
175
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  <li>
176
- <pre><%= ERB::Util.h %q| -ipglist <String>
176
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q| -ipglist <String>
177
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  Restrict search of database to list of IPGs
178
178
  * Incompatible with: subject, subject_loc| %></pre>
179
179
  </li>
180
180
  <li>
181
- <pre><%= ERB::Util.h %q| -negative_ipglist <String>
181
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q| -negative_ipglist <String>
182
182
  Restrict search of database to everything except the specified IPGs
183
183
  * Incompatible with: subject, subject_loc| %></pre>
184
184
  </li>
185
185
  <li>
186
- <pre><%= ERB::Util.h %q|-entrez_query <String>
186
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-entrez_query <String>
187
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  Restrict search with the given Entrez query
188
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  * Requires: remote| %></pre>
189
189
  </li>
190
190
  <li>
191
- <pre><%= ERB::Util.h %q|-db_soft_mask <String>
191
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-db_soft_mask <String>
192
192
  Filtering algorithm ID to apply to the BLAST database as soft masking
193
193
  * Incompatible with: db_hard_mask, subject, subject_loc| %></pre>
194
194
  </li>
195
195
  <li>
196
- <pre><%= ERB::Util.h %q|-db_hard_mask <String>
196
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-db_hard_mask <String>
197
197
  Filtering algorithm ID to apply to the BLAST database as hard masking
198
198
  * Incompatible with: db_soft_mask, subject, subject_loc| %></pre>
199
199
  </li>
200
200
  <li>
201
- <pre><%= ERB::Util.h %q|-qcov_hsp_perc <Real, 0..100>
201
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-qcov_hsp_perc <Real, 0..100>
202
202
  Percent query coverage per hsp| %></pre>
203
203
  </li>
204
204
  <li>
205
- <pre><%= ERB::Util.h %q|-max_hsps <Integer, >=1>
205
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-max_hsps <Integer, >=1>
206
206
  Set maximum number of HSPs per subject sequence to save for each query| %></pre>
207
207
  </li>
208
208
  <li>
209
- <pre><%= ERB::Util.h %q|-culling_limit <Integer, >=0>
209
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-culling_limit <Integer, >=0>
210
210
  If the query range of a hit is enveloped by that of at least this
211
211
  many higher-scoring hits, delete the hit
212
212
  * Incompatible with: best_hit_overhang, best_hit_score_edge| %></pre>
213
213
  </li>
214
214
  <li>
215
- <pre><%= ERB::Util.h %q|-best_hit_overhang <Real, (>0 and <0.5)>
215
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-best_hit_overhang <Real, (>0 and <0.5)>
216
216
  Best Hit algorithm overhang value (recommended value: 0.1)
217
217
  * Incompatible with: culling_limit| %></pre>
218
218
  </li>
219
219
  <li>
220
- <pre><%= ERB::Util.h %q|-best_hit_score_edge <Real, (>0 and <0.5)>
220
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-best_hit_score_edge <Real, (>0 and <0.5)>
221
221
  Best Hit algorithm score edge value (recommended value: 0.1)
222
222
  * Incompatible with: culling_limit| %></pre>
223
223
  </li>
224
224
  <li>
225
- <pre><%= ERB::Util.h %q|-subject_besthit
225
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-subject_besthit
226
226
  Turn on best hit per subject sequence| %></pre>
227
227
  </li>
228
228
  <li>
229
- <pre><%= ERB::Util.h %q|-max_target_seqs <Integer, >=1>
229
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-max_target_seqs <Integer, >=1>
230
230
  Maximum number of aligned sequences to keep (value of 5 or more is recommended)
231
231
  Default = '500'
232
232
  * Incompatible with: num_descriptions, num_alignments| %></pre>
@@ -235,54 +235,54 @@
235
235
 
236
236
  <br/>
237
237
 
238
- <h5>Statistical options</h5>
239
- <ul class="list-unstyled">
238
+ <h5 class="text-lg py-4 font-medium">Statistical options</h5>
239
+ <ul class="list-unstyled space-y-2">
240
240
  <li>
241
- <pre><%= ERB::Util.h %q|-dbsize <Int8>
241
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-dbsize <Int8>
242
242
  Effective length of the database| %></pre>
243
243
  </li>
244
244
  <li>
245
- <pre><%= ERB::Util.h %q|-searchsp <Int8, >=0>
245
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-searchsp <Int8, >=0>
246
246
  Effective length of the search space| %></pre>
247
247
  </li>
248
248
  </ul>
249
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250
250
  <br/>
251
251
 
252
- <h5>Extension options</h5>
253
- <ul class="list-unstyled">
252
+ <h5 class="text-lg py-4 font-medium">Extension options</h5>
253
+ <ul class="list-unstyled space-y-2">
254
254
  <li>
255
- <pre><%= ERB::Util.h %q|-xdrop_ungap <Real>
255
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-xdrop_ungap <Real>
256
256
  X-dropoff value (in bits) for ungapped extensions| %></pre>
257
257
  </li>
258
258
  <li>
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- <pre><%= ERB::Util.h %q|-xdrop_gap <Real>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-xdrop_gap <Real>
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  X-dropoff value (in bits) for preliminary gapped extensions| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-xdrop_gap_final <Real>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-xdrop_gap_final <Real>
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  X-dropoff value (in bits) for final gapped alignment| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-window_size <Integer, >=0>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-window_size <Integer, >=0>
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  Multiple hits window size, use 0 to specify 1-hit algorithm| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-ungapped
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-ungapped
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  Perform ungapped alignment only?| %></pre>
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  </li>
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  </ul>
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  <br/>
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- <h5>Miscellaneous options</h5>
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- <ul class="list-unstyled">
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+ <h5 class="text-lg py-4 font-medium">Miscellaneous options</h5>
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+ <ul class="list-unstyled space-y-2">
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  <li>
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- <pre><%= ERB::Util.h %q|-parse_deflines <Real>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-parse_deflines <Real>
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  Should the query and subject defline(s) be parsed?| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-use_sw_tback <Real>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-use_sw_tback <Real>
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  Compute locally optimal Smith-Waterman alignments?| %></pre>
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  </li>
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-
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+
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  </ul>