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comparison percolator.xml @ 2:7a0951d0e13e draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4ca7fcd1587c906db3314048a223d23b63b3f038
author galaxyp
date Fri, 10 Mar 2017 03:20:52 -0500
parents 86770eea5b09
children 07107a686ce9
comparison
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1:86770eea5b09 2:7a0951d0e13e
1 <tool id="percolator" name="Percolator" version="3.0.1"> 1 <tool id="percolator" name="Percolator" version="3.1.0">
2 <description>accurate peptide identification</description> 2 <description>accurate peptide identification</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.0">percolator</requirement> 4 <requirement type="package" version="3.1">percolator</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:"/> 7 <exit_code range="1:"/>
8 </stdio> 8 </stdio>
9 <command> 9 <command>
11 #if $output_type == "xml" 11 #if $output_type == "xml"
12 -X '$percoout' --decoy-xml-output 12 -X '$percoout' --decoy-xml-output
13 #else 13 #else
14 -J '$percoout' 14 -J '$percoout'
15 #end if 15 #end if
16 $tdmethod
16 #if $cpos 17 #if $cpos
17 -p $cpos 18 -p $cpos
18 #end if 19 #end if
19 #if $cneg 20 #if $cneg
20 -n $cneg 21 -n $cneg
35 -V $default_direction 36 -V $default_direction
36 #end if 37 #end if
37 $quickval $unitnorm $override $onlypsms 38 $quickval $unitnorm $override $onlypsms
38 </command> 39 </command>
39 <inputs> 40 <inputs>
40 <param name="output_type" label="What filetype to output" type="select" display="radio"> 41 <param name="output_type" label="What to output" type="select" display="radio">
41 <option value="xml" selected="true">percolator XML (for further processing)</option> 42 <option value="xml" selected="true">Percolator output (XML)</option>
42 <option value="tsv">Tab-separated</option> 43 <option value="tsv">Computed features of input (Tab separated)</option>
43 </param> 44 </param>
44 <param name="input" type="data" format="percin" label="Percolator input data" /> 45 <param name="input" type="data" format="percin" label="Percolator input data" />
46 <param name="tdmethod" type="select" label="Target decoy method">
47 <option value="-y" selected="true">Mix-max</option>
48 <option value="-Y">Target-decoy competition (also good when unequal amounts of target/decoy PSMs)</option>
49 </param>
45 <param name="cpos" label="Penalty for mistakes on positive examples" type="float" optional="true" /> 50 <param name="cpos" label="Penalty for mistakes on positive examples" type="float" optional="true" />
46 <param name="cneg" label="Penalty for mistakes on negative examples" type="float" optional="true" /> 51 <param name="cneg" label="Penalty for mistakes on negative examples" type="float" optional="true" />
47 <param name="trainfdr" label="FDR threshold to define positive examples" type="float" optional="true" help="Set by cross validation if 0."/> 52 <param name="trainfdr" label="FDR threshold to define positive examples" type="float" optional="true" help="Set by cross validation if 0."/>
48 <param name="testfdr" label="FDR threshold for evaluating best cross validation result" type="float" optional="true" /> 53 <param name="testfdr" label="FDR threshold for evaluating best cross validation result" type="float" optional="true" />
49 <param name="maxiter" label="Maximal number of iterations" type="integer" optional="true" /> 54 <param name="maxiter" label="Maximal number of iterations" type="integer" optional="true" />
50 <param name="quickval" label="Quicker execution by reduced internal cross-validation" type="boolean" truevalue="-x" falsevalue=""/> 55 <param name="quickval" label="Quicker execution by reduced internal cross-validation" type="boolean" truevalue="-x" falsevalue=""/>
51 <param name="default_direction" label="Most informative feature given as feature number" type="integer" optional="true" /> 56 <param name="default_direction" label="Most informative feature given as feature name." help="Can be negated to indicate lower value=better, e.g -featureName" type="text" optional="true" />
52 <param name="unitnorm" type="boolean" label="Unit normalization instead of standard deviation" truevalue="-u" falsevalue=""/> 57 <param name="unitnorm" type="boolean" label="Unit normalization instead of standard deviation" truevalue="-u" falsevalue=""/>
53 <param name="override" label="Override error check?" help="and no fallback on default score vector in case of suspect score vector" type="boolean" truevalue="-O" falsevalue=""/> 58 <param name="override" label="Override error check?" help="and no fallback on default score vector in case of suspect score vector" type="boolean" truevalue="-O" falsevalue=""/>
54 <param name="seed" label="Seed of random number generator" type="integer" optional="true" /> 59 <param name="seed" label="Seed of random number generator" type="integer" optional="true" />
55 <!--<param name="klammer" label="Retention time features calculated as in Klammer et al?" type="boolean" /> TODO: this param goes together with the doc param which I havent figured out how to use yet. --> 60 <!--<param name="klammer" label="Retention time features calculated as in Klammer et al?" type="boolean" /> TODO: this param goes together with the doc param which I havent figured out how to use yet. -->
56 <param name="onlypsms" label="Skip all outputs except PSMs" type="boolean" truevalue="-U" falsevalue=""/> 61 <param name="onlypsms" label="Skip all outputs except PSMs" type="boolean" truevalue="-U" falsevalue=""/>
68 <param name="output_type" value="xml" /> 73 <param name="output_type" value="xml" />
69 <output name="percoout" value="percolatorOut.xml" lines_diff="2" /> 74 <output name="percoout" value="percolatorOut.xml" lines_diff="2" />
70 </test> 75 </test>
71 <test> 76 <test>
72 <param name="input" value="percolatorTab" /> 77 <param name="input" value="percolatorTab" />
78 <param name="output_type" value="xml" />
79 <param name="tdmethod" value="-Y" />
80 <param name="cpos" value="0.00001" />
81 <param name="cneg" value="0.00001" />
82 <param name="trainfdr" value="0.1" />
83 <param name="testfdr" value="0.1" />
84 <param name="maxiter" value="5" />
85 <param name="quickval" value="-x" />
86 <param name="default_direction" value="RawScore" />
87 <param name="unitnorm" value="-u" />
88 <param name="override" value="-O" />
89 <param name="seed" value="2" />
90 <param name="onlypsms" value="-U" />
91 <output name="percoout" value="percolatorOut_alloptions.xml" lines_diff="2" />
92 </test>
93 <test>
94 <param name="input" value="percolatorTab" />
73 <param name="output_type" value="tsv" /> 95 <param name="output_type" value="tsv" />
74 <output name="percoout" value="percolatorOut.txt" /> 96 <output name="percoout" value="percolatorOut.txt" lines_diff="1" />
75 </test> 97 </test>
76 </tests> 98 </tests>
77 <help>The first step in analyzing an mass spectrometry assay is to match the harvested spectra against a target database using database search engines such as Sequest and Mascot, a process that renders list of peptide-spectrum matches. However, it is not trivial to assess the accuracy of these identifications. 99 <help>The first step in analyzing an mass spectrometry assay is to match the harvested spectra against a target database using database search engines such as Sequest and Mascot, a process that renders list of peptide-spectrum matches. However, it is not trivial to assess the accuracy of these identifications.
78 100
79 Percolator uses a semi-supervised machine learning to discriminate correct from incorrect peptide-spectrum matches, and calculates accurate statistics such as q-value (FDR) and posterior error probabilities. 101 Percolator uses a semi-supervised machine learning to discriminate correct from incorrect peptide-spectrum matches, and calculates accurate statistics such as q-value (FDR) and posterior error probabilities.