pyopenms 2.3.0__zip

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Hardkloer.ttd

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+<ttd>
+	<tool status="external">
+		<category>FeatureFinding</category>
+		<type>hardklor</type>
+		<external>
+      <text>
+        <onstartup>Calling Hardklor ... Wrapper was tested with "Hardklor" v1.34, report issues to the OpenMS team at www.OpenMS.de</onstartup>
+        <onfail>Please check everything ... this is still work in progress.</onfail>
+        <onfinish>Hardklor finished successfully.</onfinish>
+      </text>    
+		  <e_category>FeatureFinding</e_category>
+      <!-- ignored following options
+       -m %8
+       -s %14
+       -sc %15 %16
+       -w %20 %21 
+       %28 is an additional parameter for user specified input to hardklor (see ignored parameters)
+       
+       NOTE: Input and output need to be the first parameters to avoid 
+             runtime problems
+       -->
+		  <cloptions> "%23" "%24" -a %1 -cdm %2 -chMin %3 -chMax %4 -corr %5 -d %6 -hdat "%7" -mdat "%9" %10 -p %11 -res %12 %13 -sl %17 -sn %18 -snWin %19 -win %22 %26 %25 %28</cloptions>
+		  <path>hardklor</path>
+      <workingdirectory>.</workingdirectory>
+		  <mappings>
+			<mapping id="1" cl="%%algorithm" />
+			<mapping id="2" cl="%%charge_state_determination" />
+      <mapping id="3" cl="%%chMin" />
+      <mapping id="4" cl="%%chMax" />
+      <mapping id="5" cl="%%correlation" />
+      <mapping id="6" cl="%%depth" />
+      <mapping id="7" cl="%%hdat" />
+      <!-- <mapping id="8" cl="%%modification" /> -->
+      <mapping id="9" cl="%%mdat" />
+      <mapping id="10" cl="%%mF" />
+      <mapping id="11" cl="%%p" />
+      <mapping id="12" cl="%%resolution" />
+      <mapping id="13" cl="%%resolution_type" />
+      <!-- <mapping id="14" cl="%%s" /> -->
+      <!-- <mapping id="15" cl="%%scan_min" /> -->
+      <!-- <mapping id="16" cl="%%scan_max" /> -->
+      <mapping id="17" cl="%%sl" />
+      <mapping id="18" cl="%%sn" />
+      <mapping id="19" cl="%%snWin" />
+      <!--
+      <mapping id="20" cl="%%window_min_mz" />
+      <mapping id="21" cl="%%window_max_mz" />
+      -->
+      <mapping id="22" cl="%%win" />
+      <mapping id="23" cl="%%in" />
+      <mapping id="24" cl="%%out" />    
+      <mapping id="25" cl="%%peak_detection_mode" />    
+      <mapping id="26" cl="%%flag_no_base_averagin" />        
+      <mapping id="28" cl="%%additional_parameters" />    
+		  </mappings>
+		  <ini_param>
+			<ITEM name="in" value="" type="string" description="input file in mzXML format(valid formats: &apos;mzXML&apos;)" tags="input file" />
+			<ITEM name="out" value="" type="string" description="output file in txt format(valid formats: &apos;txt&apos;)" tags="output file" />
+
+			<ITEM name="algorithm" type="string" value="Basic" description="Chooses the algorithm for analyzing combinations of multiple peptide/protein isotope distributions. There are five algorithms to choose from: &lt;br&gt;&lt;br&gt;&lt;em&gt;Basic&lt;/em&gt; - Computes all combinatorial possibilities and returns the combination with the highest score. &lt;br&gt;&lt;em&gt;FewestPeptides&lt;/em&gt; - Computes increasing depths of combinations until the score threshold is exceeded. The smallest combination exceeding the threshold is returned, preventing &apos;over-fitting&apos; of the data. &lt;br&gt; &lt;em&gt;FastFewestPeptides&lt;/em&gt; - Same as the &lt;em&gt;FewestPeptides&lt;/em&gt; algorithm, but trades memory usage for speed. Use this method if there is sufficient memory on the system.&lt;br&gt; &lt;em&gt;FewestPeptidesChoice&lt;/em&gt; - Same as the &lt;em&gt;FewestPeptides&lt;/em&gt; algorithm, but adds a heuristic to evaluate if further combinatorial analysis would produce a better score. This method can dramatically improve speed, but may not be as accurate. &lt;br&gt; &lt;em&gt;FastFewestPeptidesChoice&lt;/em&gt; - Same as the &lt;em&gt;FewestPeptidesChoice&lt;/em&gt; algorithm, but trades memory usage for speed. Use this method if there is sufficient memory on the system. &lt;br&gt; The default setting is Basic." restrictions="Basic,FewestPeptides,FastFewestPeptides,FewestPeptidesChoice,FastFewestPeptidesChoice" />
+			
+      <ITEM name="charge_state_determination" type="string" value="B" description="Chooses the charge state determination method. There are five methods to choose from: &lt;br&gt; &lt;em&gt;B&lt;/em&gt; - Basic method, assume all charge states are possible.&lt;br&gt; &lt;em&gt;F&lt;/em&gt; - Fast Fourier Transform.&lt;br&gt; &lt;em&gt;P&lt;/em&gt; - Patterson algorithm.&lt;br&gt; &lt;em&gt;Q&lt;/em&gt; - QuickCharge method, uses inverse peak distances.&lt;br&gt; &lt;em&gt;S&lt;/em&gt; - Senko method, or combined Fast Fourier Transform and Patterson algorithm.&lt;br&gt; The default setting is B." restrictions="B,F,P,Q,S" />
+      
+      <ITEM name="chMin" type="int" value="1" description="Sets the minimum charge state to look for when analyzing a spectrum. The default value is 1." restrictions="0:" />
+      <ITEM name="chMax" type="int" value="3" description="Sets the maximum charge state to look for when analyzing a spectrum. The default value is 3." restrictions="0:" />
+      <ITEM name="correlation" type="float" value="0.90" description="Sets the correlation threshold to accept a predicted isotope distribution. Valid values are any decimal value between 0.0 and 1.0, inclusive. The default value is 0.90." restrictions="0.0:1.0" />
+      
+      <ITEM name="depth" type="int" value="3" description="Sets the depth of combinatorial analysis. This is the maximum number of protein/peptide distributions that can be combined to estimate the observed data at any given spectrum segment. The default value is 3" restrictions="0:"/>
+      <ITEM name="hdat" type="string" value="" description="Gives the full path and file name of the Hardklör data file (typically Hardklor.dat) to be used in the analysis." tags="input file,required" />
+      
+      <!--
+      <ITEM name="modification" value="" type="string" description="Includes alternative averagine models in the analysis that incorporate additional atoms and/or isotopic enrichments. Modifications are represented as text strings. Inclusion of additional atoms in the model is done using by entering an atomic formula,such as: PO2 or Cl. Inclusion of isotopic enrichment to the model is done by specifying the percent enrichment (as a decimal) followed by the atom being enriched and an index of the isotope. For example, 0.75H1 specifies 75% enrichment of the first heavy isotope of hydrogen. In other words, 75% deuterium enrichment. Two or more modifications can be combined into the same model, and separated by spaces: B2 0.5B1 This parameter can also be used redundantly to include multiple alternative averagine models in a single analysis."/>
+      -->
+      
+      <ITEM name="mdat" type="string" value="" description="Gives the full path and file name of the Mercury data file (typically ISOTOPE.DAT) to be used in the analysis." tags="input file,required" />
+      <ITEM name="mF" type="string"  value="" description="Sets a filter for mzXML files. If you want to analyze only the MS2 scans in your mzXML file, specify -mF MS2. Valid values are MS1, MS2, MS3." restrictions="-mF MS1,-mF MS2,-mF MS3" />
+      
+      <ITEM name="p" type="int" value="10" description="Sets the maximum number of peptides or proteins that are estimated from the peaks found in a spectrum segment. The default value is 10." restrictions="0:" />
+      <ITEM name="resolution"  value="100000" type="float" description="Sets the resolution of the observed spectra at m/z 400. The default setting is 100000." restrictions="0.0:" />
+      <ITEM name="resolution_type" value="FTICR" type="string" description="The user must specify a mass spectrometer code. Valid codes are FTICR, OrbiTrap, TOF, and QIT. The default settings is FTICR." restrictions="FTICR,OrbiTrap,TOF,QIT" />
+      
+      <!--
+      <ITEM name="s" type="int" description="Applies polynomial Savitsky-Golay smoothing of the mass spectra prior to analysis. The integer supplied with the flag sets the width of the smoothing window. A larger width makes smoother peaks, but has more alteration of peak intensity. By default there is no smoothing."/>
+      <ITEM name="scan_min" type="int" description="Performs analysis on a specific spectrum or set of spectra in the input file. The user specifies the specta by scan number. The user may specify a single spectrum, ex: -s 523, or a range of spectra, ex: -s 300 500."/>      
+      <ITEM name="scan_max" type="int" description=""/>
+      -->
+      
+      <ITEM name="sl" type="int" value="1" description="Sets the sensitivity level. There are four levels, 0 (low), 1 (moderate), 2 (high), and 3 (max). Increasing the sensitivity may increase computation time. The default value is 1." restrictions="0:3" />
+      
+      <ITEM name="sn" type="float" value="3.0" description="Sets the signal-over-noise threshold. Any integer or decimal value greater than or equal to 0.0 is valid. The default value is 3.0." restrictions="0.0:" />
+      
+      <ITEM name="snWin" type="float" value="50.0" description="Sets the signal-over-noise window length (in m/z). Because noise may be non-uniform across a spectra, this value adjusts the segment size considered when calculating a signal-over-noise ratio. The default value is 50.0." restrictions="0.0:" />
+      
+      <!--
+      <ITEM name="window_min_mz" type="float" description="Narrows analysis to only a small window in each segment (in m/z). The user must specify the starting and ending m/z values between which the analysis will be performed. By default the whole spectrum is analyzed."/>
+      <ITEM name="window_max_mz" type="float" description=""/>
+      -->
+      
+      <ITEM name="win" type="float" value="5.0" description="Sets the maximum width of any set of peaks in a spectrum when computing the results (in m/z). Thus, if the value was 5.0, then sets of peaks greater than 5 m/z are divided into smaller sets prior to analysis. The default value is 5.0." restrictions="0.0:" />
+
+      <ITEM name="peak_detection_mode" value="-i" type="string" description="Sets peak detection. Available modes are &apos;intersection mode&apos; (-i, default) and &apos;union mode&apos; (-u). Spectra are analyzed for peaks in overlapping segments. When intersection mode is set, peaks are only accepted if they appear in two overlapping segments. When union mode is set, peaks are accepted regardless of whether they appear in one segment or two overlapping segments. Intersection is turned on by default." restrictions="-u,-i" />
+      <ITEM name="flag_no_base_averagin" value="" type="string" description="Specifies &apos;no base&apos; averagine. Only modified averagine models will be used in the analysis." restrictions=",-nb" />    
+      
+      <ITEM name="additional_parameters" value="" type="string" description="Some of the &apos;hardkloer&apos; parameters could not be translated to an appropriate representation in ttd-Format and are therefore collected in this single parameter. These parameter will be given directly to &apos;hardklor&apos; any checks or prefix. Options collected here are: &lt;br&gt;&lt;br&gt; &lt;b&gt;-w [double] [double]&lt;/b&gt; Narrows analysis to only a small window in each segment (in m/z). The user must specify the starting and ending m/z values between which the analysis will be performed. By default the whole spectrum is analyzed.&apos; &lt;br&gt;&lt;br&gt; &lt;b&gt;-s [int] &lt;/b&gt; Applies polynomial Savitsky-Golay smoothing of the mass spectra prior to analysis. The integer supplied with the flag sets the width of the smoothing window. A larger width makes smoother peaks, but has more alteration of peak intensity. By default there is no smoothing. &lt;br&gt;&lt;br&gt; &lt;b&gt;-sc [int] [int]&lt;/b&gt; Performs analysis on a specific spectrum or set of spectra in the input file. The user specifies the specta by scan number. The user may specify a single spectrum, ex: -sc 523, or a range of spectra, ex: -sc 300 500 &lt;br&gt;&lt;br&gt; &lt;b&gt;-m [modification]&lt;/b&gt; Includes alternative averagine models in the analysis that incorporate additional atoms and/or isotopic enrichments. Modifications are represented as text strings. Inclusion of additional atoms in the model is done using by entering an atomic formula,such as: PO2 or Cl. Inclusion of isotopic enrichment to the model is done by specifying the percent enrichment (as a decimal) followed by the atom being enriched and an index of the isotope. For example, 0.75H1 specifies 75% enrichment of the first heavy isotope of hydrogen. In other words, 75% deuterium enrichment. Two or more modifications can be combined into the same model, and separated by spaces: B2 0.5B1 This parameter can also be used redundantly to include multiple alternative averagine models in a single analysis." tags="advanced" />    
+     
+		  </ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/LINUX/TPP_ProteinProphet.ttd

@@ -0,0 +1,46 @@
+<ttd>
+	<tool status="external">
+		<category>does not really matter</category>
+		<type>TPP_ProteinProphet</type>
+		<external>
+      <text>
+        <onstartup>Calling TPP's ProteinProphet... Wrapper tested with TPP v4.4.1 (VUVUZELA), report issues to the OpenMS team at www.OpenMS.de</onstartup>
+        <onfail>Something went wrong. Possible cause: You forgot to call TPP's 'RefreshParser' prior to calling this?</onfail>
+        <onfinish>Tool finished successfully.</onfinish>
+      </text>
+		  <e_category>Protein/Peptide Identification</e_category>
+		  <cloptions>"%1" %2 EXCELPEPS %4 %6 %7 %8 %9 %10 %11</cloptions>
+		  <path>ProteinProphet</path>
+      <workingdirectory>.</workingdirectory>
+		  <mappings>
+			<mapping id="1" cl="%%in" />
+			<mapping id="2" cl="MINPROB %%min_prob" />
+			<mapping id="4" cl="EXCEL%%excel_minprob" />
+			<mapping id="6" cl="%%flag_delude" />
+			<mapping id="7" cl="%%flag_normprotlen" />
+			<mapping id="8" cl="%%flag_logprobs" />
+			<mapping id="9" cl="%%flag_confem" />
+			<mapping id="10" cl="%%flag_allpeps" />
+			<mapping id="11" cl="%%flag_noplot" />
+			<file_post location="%WORKINGDIR/0.prot.xml" target="out" />
+			<file_post location="%WORKINGDIR/0.prot.xls" target="out_xls" />
+		  </mappings>
+		  <ini_param>
+			<ITEM name="in" value="" type="string" description="Input file in pepXML format(valid formats: &apos;pepXML&apos;)" tags="input file,required" />
+			<ITEM name="out" value="" type="string" description="Output file in protXML format(valid formats: &apos;protXML&apos;)" tags="output file" />
+			<ITEM name="out_xls" value="" type="string" description="Output file in XLS format(valid formats: &apos;xls&apos;)." tags="output file" />
+
+			<ITEM name="min_prob" value="0.05" type="float" description="PeptideProphet (or any other) probabilty threshold"/>
+			<ITEM name="excel_minprob" value="0.0" type="float" description="Write output tab delim xls file including all protein (group)s with minimum probability (only meaningful when 'flag_excel' is set)." restrictions="0:1" tags=""/>
+
+			<ITEM name="flag_occam" value="" type="string" description="Do not use Occam's Razor to derive the simplest protein list to explain observed peptides" tags="" restrictions=",NOOCCAM" />
+			<ITEM name="flag_delude" value="" type="string" description="Do NOT use peptide degeneracy information when assessing proteins" tags="" restrictions=",DELUDE" />
+			<ITEM name="flag_normprotlen" value="" type="string" description="Normalize NSP using protein length" tags="" restrictions=",NORMPROTLEN" />
+			<ITEM name="flag_logprobs" value="" type="string" description="Use the log of the probabilities in the confidence calculations" tags="" restrictions=",LOGPROBS" />
+			<ITEM name="flag_confem" value="" type="string" description="Use the EM to compute probability given the confidence" tags="" restrictions=",CONFEM" />
+			<ITEM name="flag_allpeps" value="" type="string" description="Consider all possible peptides in the database in the confidence model" tags="" restrictions=",ALLPEPS" />
+			<ITEM name="flag_noplot" value="" type="string" description="do not generate plot png file" tags="" restrictions=",NOPLOT" />
+		  </ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/LINUX/mail.ttd

@@ -0,0 +1,22 @@
+<ttd>
+	<tool status="external">
+		<category></category>
+		<type>mail</type>
+		<external>
+		  <e_category>MailNotify</e_category>
+		  <cloptions>-c "echo """%2""" | mail -s """%1""" %3"</cloptions>
+		  <path>sh</path>
+		  <mappings>
+			<mapping id="1" cl="%%subject" />
+			<mapping id="2" cl="%%body The filename is '%%in'." />
+			<mapping id="3" cl="%%mailadress" />
+		  </mappings>
+		  <ini_param>
+			<ITEM name="in" value="" type="string" description="input file which just finished and for which you want the notify-mail" tags="input file" />
+			<ITEM name="subject" value="TOPPAS notification" type="string" description="Message subject" tags="" />
+			<ITEM name="body" value="Emailing to tell you that a file just got generated." type="string" description="The body of your message" tags="" />
+			<ITEM name="mailadress" value="...@..." type="string" description="Your mail address" tags="" />
+		  </ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/MSGFtoPercolator.ttd

@@ -0,0 +1,30 @@
+<ttd>
+	<tool status="external">
+		<category>Identification</category>
+		<type>MSGFtoPercolator</type>
+		<external>
+      <text>
+        <onstartup>Running "msgf2pin" converter...</onstartup>
+        <onfail>Something went wrong. Is the msgf2pin executable globally accessible?</onfail>
+        <onfinish>msgf2pin finished successfully.</onfinish>
+      </text>    
+		  <e_category>Identification</e_category>
+		  <cloptions>--pattern "%4" --outputTab "%3" "%1" "%2"</cloptions>
+		  <path>msgf2pin</path>
+		  <workingdirectory>.</workingdirectory>
+		  <mappings>
+			<mapping id="1" cl="%%in" />
+			<mapping id="2" cl="%%in_decoy" />
+			<mapping id="3" cl="%%out" />
+            <mapping id="4" cl="%%decoy_pattern" />
+		  </mappings>
+		  <ini_param>
+			<ITEM name="in" value="" type="string" description="Input file: MS-GF+ search results; either from a combined target/decoy search (then set 'decoy_pattern') or from a target-only search (then set 'in_decoy') (valid formats: 'mzid')" tags="input file" />
+			<ITEM name="in_decoy" value="" type="string" description="Input file: MS-GF+ search results; from a decoy-only search (valid formats: 'mzid')" tags="input file" />
+			<ITEM name="out" value="" type="string" description="Output file: Percolator tab-delimited input (valid formats: 'csv')" tags="output file" />
+            <ITEM name="decoy_pattern" value="DECOY_" type="string" description="Pattern identifying decoy matches. Ignored if 'in_decoy' is set, but must not be empty!" />
+            <ITEM name="enzyme" value="trypsin" type="string" description="Enzyme used for digestion" restrictions="no_enzyme,elastase,pepsin,proteinasek,thermolysin,chymotrypsin,lys-n,lys-c,arg-c,asp-n,glu-c,trypsin" />
+		  </ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/MascotPercolator.ttd

@@ -0,0 +1,42 @@
+<ttd>
+	<tool status="external">
+		<category>Identification</category>
+		<type>MascotPercolator</type>
+		<external>
+      <text>
+        <onstartup>Running Mascot Percolator...</onstartup>
+        <onfail>Something went wrong. Is Java 8 available?</onfail>
+        <onfinish>Mascot Percolator finished successfully.</onfinish>
+      </text>    
+		  <e_category>Identification</e_category>
+		  <cloptions>-Xmx%6m -cp "%5" cli.MascotPercolator -i1 -newDat -overwrite -summary -u -target "%1" -decoy "%2" -out "%3" -decoypattern "%4"</cloptions>
+		  <path>java</path>
+		  <workingdirectory>.</workingdirectory>
+		  <mappings>
+			<mapping id="1" cl="%%in" />
+			<mapping id="2" cl="%%in_decoy" />
+			<mapping id="3" cl="%TMP/%BASENAME[%%in]" />
+            <mapping id="4" cl="%%decoy_pattern" />
+            <mapping id="5" cl="%%jar" />
+            <mapping id="6" cl="%%java_memory" />
+			<file_post location="%TMP/%BASENAME[%%in].psms" target="out" />
+			<file_post location="%TMP/%BASENAME[%%in]_decoy.psms" target="out_decoy" />
+			<file_post location="%TMP/%BASENAME[%%in].summary.txt" target="out_summary" />
+			<file_post location="%TMP/%BASENAME[%%in].summary_decoy.txt" target="out_summary_decoy" />
+			<file_post location="%TMP/%BASENAME[%%in].datp" target="out_dat" />
+          </mappings>
+		  <ini_param>
+			<ITEM name="in" value="" type="string" description="Input file: Mascot search results from MascotAdapterOnline; either from a combined target/decoy search (then set 'decoy_pattern') or from a target-only search (then set 'in_decoy') (valid formats: 'idXML')" tags="input file" />
+			<ITEM name="in_decoy" value="TARGET" type="string" description="Input file: Mascot decoy-only search results from MascotAdapterOnline, or 'TARGET' for a concatenated target/decoy search passed via 'in_target' (valid formats: 'idXML')" tags="input file" />
+			<ITEM name="jar" value="MascotPercolator.jar" type="string" description="Mascot Percolator .jar file (valid formats: 'jar')" tags="input file" />
+			<ITEM name="out" value="" type="string" description="Output file: Percolator tab-delimited output, target hits (valid formats: 'psms')" tags="output file" />
+			<ITEM name="out_decoy" value="" type="string" description="Output file: Percolator tab-delimited output, decoy hits (valid formats: 'psms')" tags="output file" />
+			<ITEM name="out_summary" value="" type="string" description="Output file: Mascot Percolator tab-delimited output, target summary (valid formats: 'txt')" tags="output file" />
+			<ITEM name="out_summary_decoy" value="" type="string" description="Output file: Mascot Percolator tab-delimited output, decoy summary (valid formats: 'txt')" tags="output file" />
+			<ITEM name="out_dat" value="" type="string" description="Output file: Mascot DAT file with Percolator scores (valid formats: 'datp')" tags="output file" />
+            <ITEM name="decoy_pattern" value="DECOY_" type="string" description="Pattern identifying decoy matches. Only used if 'in_decoy' is 'TARGET', but must not be empty!" />
+            <ITEM name="java_memory" value="1024" type="string" description="Maximum Java heap size (in MB)" />            
+		  </ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Percolator.ttd

@@ -0,0 +1,29 @@
+<ttd>
+	<tool status="external">
+		<category>Identification</category>
+		<type>Percolator</type>
+		<external>
+      <text>
+        <onstartup>Running Percolator...</onstartup>
+        <onfail>Something went wrong. Is the Percolator executable globally accessible?</onfail>
+        <onfinish>Percolator finished successfully.</onfinish>
+      </text>    
+		  <e_category>Identification</e_category>
+		  <cloptions>--only-psms --results-psms "%2" --decoy-results-psms "%3" "%1"</cloptions>
+		  <path>percolator</path>
+		  <workingdirectory>.</workingdirectory>
+		  <mappings>
+			<mapping id="1" cl="%%in" />
+			<mapping id="2" cl="%TMP/%BASENAME[%%in].psms" />
+			<mapping id="3" cl="%TMP/%BASENAME[%%in]_decoy.psms" />
+			<file_post location="%TMP/%BASENAME[%%in].psms" target="out" />
+			<file_post location="%TMP/%BASENAME[%%in]_decoy.psms" target="out_decoy" />
+		  </mappings>
+		  <ini_param>
+			<ITEM name="in" value="" type="string" description="Input file: Percolator tab-delimited input (valid formats: 'csv')" tags="input file" />
+			<ITEM name="out" value="" type="string" description="Output file: Percolator tab-delimited output, target hits (valid formats: 'psms')" tags="output file" />
+			<ITEM name="out_decoy" value="" type="string" description="Output file: Percolator tab-delimited output, decoy hits (valid formats: 'psms')" tags="output file" />
+		  </ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/QCExporter.ttd

@@ -0,0 +1,51 @@
+<ttd>
+	<tool status="external">
+		<category>does not really matter</category>
+		<type>QCMLExport</type>
+		<external>
+				<text>
+					<onstartup>Calling python QCExporter ...</onstartup>
+					<onfail>Something went wrong. Is 'python' in your PATH?</onfail>
+					<onfinish>Tool finished successfully.</onfinish>
+				</text>
+			<e_category>FileConversion</e_category>
+			<cloptions> "%1"/QCExporter.py "%2" "%3" "%4" "%5" "%6" "%7" "%8" "%9" "%10"</cloptions>
+			<path>python</path>
+			<mappings>
+				<mapping id="1" cl="%%scriptpath" />
+				<mapping id="2" cl="%TMP" />
+				<mapping id="3" cl="%%inML" />
+				<mapping id="4" cl="%%inID" />
+				<mapping id="5" cl="%%inTSVspec" />
+				<mapping id="6" cl="%%inTSVtic" />
+				<mapping id="7" cl="%%inTSVacc" />
+				<mapping id="8" cl="%%inFIGspec" />
+				<mapping id="9" cl="%%inFIGtic" />
+				<mapping id="10" cl="%%inFIGacc" />
+				<file_post location="%TMP/genericwrapper.qcML" target="out" />
+			</mappings>
+			<ini_param>
+				<ITEM name="scriptpath" value="." type="string" description="input script path, this should point
+to share/OpenMS/SCRIPTS of your OpenMS installation"/>
+				<ITEM name="inML" value="" type="string" description="input file in mzML format(valid formats:
+&apos;mzML&apos;)" tags="input file" />
+				<ITEM name="inID" value="" type="string" description="input file in id format(valid formats:
+&apos;idXML&apos;)" tags="input file" />
+				<ITEM name="inTSVspec" value="" type="string" description="tabular input data for precursor stats(valid formats:
+&apos;unknown,tsv&apos;)" tags="input file" />
+				<ITEM name="inTSVtic" value="" type="string" description="tabular input data for tic stats(valid formats:
+&apos;unknown,tsv&apos;)" tags="input file" />
+				<ITEM name="inTSVacc" value="" type="string" description="tabular input data for accuracy stats(valid formats:
+&apos;unknown,tsv&apos;)" tags="input file" />
+				<ITEM name="inFIGspec" value="" type="string" description="R figure for precursor stats(valid formats:
+&apos;unknown,tsv&apos;)" tags="input file" />
+				<ITEM name="inFIGtic" value="" type="string" description="R figure for tic stats(valid formats:
+&apos;unknown,tsv&apos;)" tags="input file" />
+				<ITEM name="inFIGacc" value="" type="string" description="R figure for accuracy stats(valid formats:
+&apos;unknown,tsv&apos;)" tags="input file" />
+				<ITEM name="out" value="" type="string" description="output file in qcML format(valid formats:
+&apos;qcML&apos;)" tags="output file" />
+			</ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/RawDirConvert.ttd

@@ -0,0 +1,25 @@
+<ttd>
+	<tool status="external">
+		<category>does not really matter</category>
+		<type>RAWDirConvert</type>
+		<external>
+      <text>
+        <onstartup>Calling PWiz' msconvert for directory-based raw files ...</onstartup>
+        <onfail>Something went wrong. Is 'msconvert' in your PATH?</onfail>
+        <onfinish>Tool finished successfully.</onfinish>
+      </text>    
+		  <e_category>FileConversion</e_category>
+		  <cloptions>-o "%1" --mzML "%2"</cloptions>
+		  <path>msconvert</path>
+		  <mappings>
+			<mapping id="1" cl="%TMP" />
+			<mapping id="2" cl="%DIR[%%in]" />
+			<file_post location="%TMP/%BASENAME[%DIR[%%in]].mzML" target="out" />
+		  </mappings>
+		  <ini_param>
+			<ITEM name="in" value="" type="string" description="Exemplary file in raw folder (e.g., headers.txt in Waters raw folders)" tags="input file" />
+			<ITEM name="out" value="" type="string" description="output file in mzML format(valid formats: &apos;mzML&apos;)" tags="output file" />
+		  </ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/ReadMe.txt

@@ -0,0 +1,72 @@
+This ReadMe describes how OpenMS deals with TOPP tool description (*.ttd) files and the external tools wrapped by them.
+
+== General ==
+
+Using *.ttd files OpenMS can be instructed to run external tools (like msconvert from Proteowizard) in a convenient way.
+Each *.ttd file can contain one or more <tool> sections, each telling OpenMS how to call the respective tool.
+You can then use our TOPP tool
+
+  GenericWrapper
+
+to run the external tool.
+GenericWrapper will dynamically change its available '-type' parameter list, depending on the *.ttd files present in this folder.
+
+The name of the *.ttd file does not really matter, but it should be descriptive.
+
+This way you can now easily integrate external tools into TOPPAS, by just adding a GenericWrapper node of the desired '-type'.
+
+===============
+== For Users ==
+===============
+
+If you want to add a custom *.ttd file (obtainable from our website or other users), simply add it to this folder.
+Some tools (like 'mail' on linux), might only be available on certain Operating Systems. In this case you should
+place them in the respective subfolder. The folder of this ReadMe and the subfolder matching your Operating System will be
+scanned for *.ttd files.
+Additionally you can create an environment variable OPENMS_TTD_PATH and use it to point to one (!) custom directory of your choice.
+This is useful when upgrading OpenMS to another version while keeping all your custom *.ttd files.
+
+If you encounter a bug, file a bug report via https://github.com/OpenMS/OpenMS/issues
+and provide the output of GenericWrapper (ideally with '-debug 10' option enabled)
+and your input files (if applicable).
+
+After adding/removing *.ttd files you need to restart any open instances of TOPPAS to see the updated list of types for GenericWrapper.
+
+
+===========================
+== For experienced Users ==
+===========================
+
+Hints -- read(!):
+ - When mapping a SINGLE filename while building the command line in 'cloptions', wrap them in QUOTES! (to avoid the 'spaces in filenames' problem)
+ - When mapping a LIST of filenames (from ITEMLIST parameters) while building the command line in 'cloptions', NO NOT QUOTE! (GenericWrapper will do this automatically)
+ - Find a good name for <type> - it should be descriptive duplicate names are not allowed
+
+If you want to wrap your own tools and write custom *.ttd files,
+a good starting point is the 
+
+  TEMPLATE.ttd_
+
+file. See description inside the file.
+
+The template's suffix is 'ttd_' in order to disregard it as an active *.ttd file.
+Make a copy of it and modify to your needs.
+
+Once you are done, place the new *.ttd in either this folder (for all Operating Systems) or the correct subfolder.
+
+You can also have a look at existing wrappers and get inspiration.
+
+A note on using more complicated shell commands (e.g. piping):
+  - as we use QProcess to call the external tool, no piping and shell internal commands (such as 'echo' on Windows) are supported
+    To work around this you have to specify the command tool itself, e.g.
+	
+	<path>cmd</path>
+	<cloptions>/C "echo ""bla bla"" > testfile"</cloptions>
+	
+	or
+	
+	<path>sh</path>
+	<cloptions>-c "echo """%2""" > testfile"</cloptions>
+                  
+	Note that escaping of internal quotes works different on each platform. You need to test this!
+	

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_generic.ttd

@@ -0,0 +1,42 @@
+<ttd>
+	<tool status="external">
+		<category>does not really matter</category>
+		<type>Rscript_generic</type>
+		<external>
+				<text>
+					<onstartup>Calling Rscript with up to 4 input and 4 output files and 2 output lists</onstartup>
+					<onfail>Something went wrong. Is the 'Rscript' executable in your PATH?</onfail>
+					<onfinish>Tool finished successfully.</onfinish>
+				</text>
+			<e_category>Postprocessing</e_category>
+			<cloptions>--vanilla "%1" -in1 %2 -in2 %3 -in3 %4 -in4 %5 -out1 "%6" -out2 "%7" -out3 "%8" -out4 "%9" -outlist1 %10 -outlist2 %11</cloptions>
+			<path>Rscript</path>
+			<mappings>
+				<mapping id="1" cl="%%file_script" />
+				<mapping id="2" cl="%%in1" />
+				<mapping id="3" cl="%%in2" />
+				<mapping id="4" cl="%%in3" />
+				<mapping id="5" cl="%%in4" />
+				<mapping id="6" cl="%%out1" />
+				<mapping id="7" cl="%%out2" />
+				<mapping id="8" cl="%%out3" />
+				<mapping id="9" cl="%%out4" />
+				<mapping id="10" cl="%%outlist1" />
+				<mapping id="11" cl="%%outlist2" />
+			</mappings>
+			<ini_param>
+				<ITEM name="file_script" value="" type="string" description="input R script; an example is provided in share/OpenMS/SCRIPTS/Rscript_generic_example.R" tags="input file"/>
+				<ITEMLIST name="in1" type="input-file" description="Input file(s) separated by blanks" required="false" advanced="false"></ITEMLIST>
+				<ITEMLIST name="in2" type="input-file" description="Input file(s) separated by blanks" required="false" advanced="false"></ITEMLIST>
+				<ITEMLIST name="in3" type="input-file" description="Input file(s) separated by blanks" required="false" advanced="false"></ITEMLIST>
+				<ITEMLIST name="in4" type="input-file" description="Input file(s) separated by blanks" required="false" advanced="false"></ITEMLIST>
+				<ITEM name="out1" value="" type="output-file" description="Output file which your R script writes to" required="false" advanced="false" />
+				<ITEM name="out2" value="" type="output-file" description="Output file which your R script writes to" required="false" advanced="false" />
+				<ITEM name="out3" value="" type="output-file" description="Output file which your R script writes to" required="false" advanced="false" />
+				<ITEM name="out4" value="" type="output-file" description="Output file which your R script writes to" required="false" advanced="false" />
+				<ITEMLIST name="outlist1" type="output-file" description="Output file(s) separated by blanks" required="false" advanced="false"></ITEMLIST>
+				<ITEMLIST name="outlist2" type="output-file" description="Output file(s) separated by blanks" required="false" advanced="false"></ITEMLIST>
+			</ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_mzTab2tsv_PEP.ttd

@@ -0,0 +1,26 @@
+<ttd>
+	<tool status="external">
+		<category>does not really matter</category>
+		<type>Rscript_mzTab2tsv_PEP</type>
+		<external>
+				<text>
+					<onstartup>Calling Rscript mzTab2tsv_PEP ...</onstartup>
+					<onfail>Something went wrong. Is 'R' in your PATH?</onfail>
+					<onfinish>Tool finished successfully.</onfinish>
+				</text>
+			<e_category>FileConversion</e_category>
+			<cloptions>--vanilla "%1/mzTab2tsv_PEP.R" "%2" "%3"</cloptions>
+			<path>Rscript</path>
+			<mappings>
+				<mapping id="1" cl="%%scriptpath" />
+				<mapping id="2" cl="%%in" />
+				<mapping id="3" cl="%%out" />
+			</mappings>
+			<ini_param>
+				<ITEM name="scriptpath" value="." type="string" description="input script path, this should point to share/OpenMS/SCRIPTS of your OpenMS installation"/>
+				<ITEM name="in" value="" type="input-file" description="tabular input data" required="true" advanced="false" supported_formats="*.tsv" />
+				<ITEM name="out" value="" type="output-file" description="output tsv file" required="true" advanced="false" supported_formats="*.tsv" />
+			</ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_mzTab2tsv_PRT.ttd

@@ -0,0 +1,26 @@
+<ttd>
+	<tool status="external">
+		<category>does not really matter</category>
+		<type>Rscript_mzTab2tsv_PRT</type>
+		<external>
+				<text>
+					<onstartup>Calling Rscript mzTab2tsv_PRT ...</onstartup>
+					<onfail>Something went wrong. Is 'R' in your PATH?</onfail>
+					<onfinish>Tool finished successfully.</onfinish>
+				</text>
+			<e_category>FileConversion</e_category>
+			<cloptions>--vanilla "%1/mzTab2tsv_PRT.R" "%2" "%3"</cloptions>
+			<path>Rscript</path>
+			<mappings>
+				<mapping id="1" cl="%%scriptpath" />
+				<mapping id="2" cl="%%in" />
+				<mapping id="3" cl="%%out" />
+			</mappings>
+			<ini_param>
+				<ITEM name="scriptpath" value="." type="string" description="input script path, this should point to share/OpenMS/SCRIPTS of your OpenMS installation"/>
+				<ITEM name="in" value="" type="input-file" description="tabular input data" required="true" advanced="false" supported_formats="*.tsv" />
+				<ITEM name="out" value="" type="output-file" description="output tsv file" required="true" advanced="false" supported_formats="*.tsv" />
+			</ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_mzTab2tsv_PSM.ttd

@@ -0,0 +1,26 @@
+<ttd>
+	<tool status="external">
+		<category>does not really matter</category>
+		<type>Rscript_mzTab2tsv_PSM</type>
+		<external>
+				<text>
+					<onstartup>Calling Rscript mzTab2tsv_PSM ...</onstartup>
+					<onfail>Something went wrong. Is 'R' in your PATH?</onfail>
+					<onfinish>Tool finished successfully.</onfinish>
+				</text>
+			<e_category>FileConversion</e_category>
+			<cloptions>--vanilla "%1/mzTab2tsv_PSM.R" "%2" "%3"</cloptions>
+			<path>Rscript</path>
+			<mappings>
+				<mapping id="1" cl="%%scriptpath" />
+				<mapping id="2" cl="%%in" />
+				<mapping id="3" cl="%%out" />
+			</mappings>
+			<ini_param>
+				<ITEM name="scriptpath" value="." type="string" description="input script path, this should point to share/OpenMS/SCRIPTS of your OpenMS installation"/>
+				<ITEM name="in" value="" type="input-file" description="tabular input data" required="true" advanced="false" supported_formats="*.tsv" />
+				<ITEM name="out" value="" type="output-file" description="output tsv file" required="true" advanced="false" supported_formats="*.tsv" />
+			</ini_param>
+		</external>
+	</tool>
+</ttd>

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/TOOLS/EXTERNAL/Rscript_qcfigures_acc.ttd

@@ -0,0 +1,30 @@
+<ttd>
+	<tool status="external">
+		<category>does not really matter</category>
+		<type>Rscript_qcfigures_acc</type>
+		<external>
+				<text>
+					<onstartup>Calling Rscript acc ...</onstartup>
+					<onfail>Something went wrong. Is 'R' in your PATH?</onfail>
+					<onfinish>Tool finished successfully.</onfinish>
+				</text>
+			<e_category>FileConversion</e_category>
+			<cloptions>--vanilla "%1/ProduceQCFigures_acc.R" "%2" "%3"</cloptions>
+			<path>Rscript</path>
+			<mappings>
+				<mapping id="1" cl="%%scriptpath" />
+				<mapping id="2" cl="%%inTSVacc" />
+				<mapping id="3" cl="%TMP/%BASENAME[%%inTSVacc]_acc.png" />
+				<file_post location="%TMP/%BASENAME[%%inTSVacc]_acc.png" target="out" />
+			</mappings>
+			<ini_param>
+				<ITEM name="scriptpath" value="." type="string" description="input script path, this should point
+to share/OpenMS/SCRIPTS of your OpenMS installation"/>
+				<ITEM name="inTSVacc" value="" type="string" description="tabular input data for accuracy stats(valid formats:
+&apos;unknown,tsv&apos;)" tags="input file" />
+				<ITEM name="out" value="" type="string" description="output figure from R(valid formats:
+&apos;png&apos;)" tags="output file" />
+			</ini_param>
+		</external>
+	</tool>
+</ttd>