Mercurial > repos > galaxyp > proteomiqon_proteininference

annotate proteomiqon_proteininference.xml @ 1:7729b9043b80 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 6c26a48bade20a6be46dec57602579ffc05cbe27"
author galaxyp
date Fri, 29 Apr 2022 19:29:14 +0000
parents 8e4fb95a319a
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8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
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1 <tool id="proteomiqon_proteininference" name="ProteomIQon ProteinInference" version="@VERSION@" profile="20.05">
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2 <description>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
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3 uses identified peptides to infere proteins explaining their presence in the sample.
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
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4 </description>
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5 <macros>
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6 <token name="@VERSION@">0.0.7</token>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@VERSION@">proteomiqon-proteininference</requirement>
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10 </requirements>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
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11 <command detect_errors="exit_code"><![CDATA[
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
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12 #import re
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
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13 #if $PSMInputModeCond.PSMInputMode == "single"
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14 #set basename = $re.sub(r'[^\w ,.\-+]','_',$PSMInputModeCond.scoredPSMs.element_identifier)
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15 ln -s '$scoredPSMs' '${basename}.qpsm' &&
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16 mkdir './out' &&
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17 ln -s '$out_prot' './out/${basename}.prot' &&
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18 #elif $PSMInputModeCond.PSMInputMode == "multi"
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19 #for $psmfile in $PSMInputModeCond.scoredPSMs
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20 #set basename = $re.sub(r'[^\w ,.\-+]','_',$psmfile.element_identifier)
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21 ln -s '$psmfile' '${basename}.qpsm' &&
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22 #end for
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23 #end if
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24 #if $outputParamfile:
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25 cat '$paramfile' >> '$out_paramfile' &&
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26 #end if
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27 proteomiqon-proteininference -i './' -d '$peptideDB' -p '$paramfile' -o './out'
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
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28 ]]>
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29 </command>
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30 <configfiles>
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31 <configfile name="paramfile">
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32 <![CDATA[
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
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33 {
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
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34 "ProteinIdentifierRegex": "${ProteinIdentifierRegex}",
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35 "Protein": {
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36 "Case": "${Protein}"
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37 },
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38 "Peptide": {
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39 "Case": "${Peptide}"
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40 },
1
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41 #if $PSMInputModeCond.PSMInputMode == "multi"
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42 "GroupFiles": ${PSMInputModeCond.GroupFiles},
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43 #else
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44 "GroupFiles": false,
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45 #end if
0
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46 #if $GetQValueCond.GetQValue == "LogisticRegression"
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47 "GetQValue": {
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48 "Case": "${GetQValueCond.GetQValue}",
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49 "Fields": [
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50 {
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
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51 "Case": "${GetQValueCond.LogisticRegressionType}"
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52 }
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53 ]
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
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54 }
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
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55 #else
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56 "GetQValue": {
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57 "Case": "${GetQValueCond.GetQValue}",
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58 }
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59 #end if
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60 }
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61 ]]>
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62 </configfile>
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63 </configfiles>
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64 <inputs>
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65 <param name="peptideDB" type="data" format="sqlite" label="Peptide database" help="Specify the peptide data base."/>
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66 <conditional name="PSMInputModeCond">
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67 <param name="PSMInputMode" type="select" label="PSM file input mode">
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68 <option value="single">Single File</option>
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69 <option value="multi">Multiple Files</option>
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70 </param>
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71 <when value="single">
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72 <param name="scoredPSMs" type="data" format="tabular" label="Scored PSM file" help="Specify peptide identifications." />
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73 </when>
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74 <when value="multi">
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75 <param name="scoredPSMs" type="data" format="tabular" label="Scored PSM files" help="Specify list of peptide identifications." multiple="true"/>
1
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76 <param name="GroupFiles" type="boolean" checked="true" label="Groupe files" help="If checked, protein inference is carried out using peptide information from all files simultaneously."/>
0
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77 </when>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
78 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
79 <param name="ProteinIdentifierRegex" type="text" value="id" label="Protein identifier regex pattern" help="Fasta headers do often contain additional information in addition to your protein identifier, by specifying a regex pattern the tool can extract the protein IDs. If you fasta headers are already cleaned you can leave this field empty.">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
80 <sanitizer sanitize="false" />
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
81 </param>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
82 <param name="Protein" type="select" label="Protein" help="Specify how protein groups are created. For details please refer to the description below.">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
83 <option value="Minimal">Minimal</option>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
84 <option value="Maximal" selected="true">Maximal</option>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
85 </param>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
86 <param name="Peptide" type="select" label="Peptide" help="Specify how peptides are used to infer protein groups. For details please refer to the description below.">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
87 <option value="Minimal" selected="true">Minimal</option>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
88 <option value="Maximal">Maximal</option>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
89 <option value="MaximalInverse">MaximalInverse</option>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
90 </param>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
91 <conditional name="GetQValueCond">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
92 <param name="GetQValue" type="select" label="Q-Value method" help="Specify if and how q-value calculation should be carried out.">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
93 <option value="Storey" selected="true">Storey</option>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
94 <option value="LogisticRegression">Logistic Regression</option>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
95 <option value="NoQValue">NoQValue</option>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
96 </param>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
97 <when value="Storey"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
98 <when value="LogisticRegression">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
99 <param name="LogisticRegressionType" type="select" label="Logistic regression type">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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100 <option value="Conservative">Conservative</option>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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101 <option value="MAYU" selected="true">MAYU</option>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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102 <option value="DecoyTargetRatio">DecoyTargetRatio</option>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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103 </param>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
104 </when>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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105 <when value="NoQValue"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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106 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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107 <param name="outputParamfile" type="boolean" value="false" label="Output parameter file"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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108 </inputs>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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109 <outputs>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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110 <data format="tabular" name="out_prot" >
1
7729b9043b80 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 6c26a48bade20a6be46dec57602579ffc05cbe27"
galaxyp
parents: 0
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111 <filter>PSMInputModeCond['PSMInputMode'] == 'single'</filter>
0
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
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112 </data>
1
7729b9043b80 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 6c26a48bade20a6be46dec57602579ffc05cbe27"
galaxyp
parents: 0
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113 <collection type="list" format="tabular" name="out_prot_collection" >
7729b9043b80 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 6c26a48bade20a6be46dec57602579ffc05cbe27"
galaxyp
parents: 0
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114 <discover_datasets pattern="(?P&lt;designation&gt;.+\.prot)" directory="out" />
7729b9043b80 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 6c26a48bade20a6be46dec57602579ffc05cbe27"
galaxyp
parents: 0
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115 <filter>PSMInputModeCond['PSMInputMode'] == 'multi'</filter>
7729b9043b80 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 6c26a48bade20a6be46dec57602579ffc05cbe27"
galaxyp
parents: 0
diff changeset
116 </collection>
0
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
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117 <data format="json" name="out_paramfile">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
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118 <filter>outputParamfile</filter>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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119 </data>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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120 </outputs>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
121 <tests>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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122 <test expect_num_outputs="1">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
123 <param name="peptideDB" value="sample.db"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
124 <conditional name="PSMInputModeCond">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
125 <param name="PSMInputMode" value="single"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
126 <param name="scoredPSMs" value="sample_1.qpsm"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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127 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
128 <param name="ProteinIdentifierRegex" value="id"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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129 <param name="Protein" value="Minimal"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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130 <param name="Peptide" value="Minimal"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
131 <param name="outputParamfile" value="false"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
132 </test>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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133 <test expect_num_outputs="2">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
134 <param name="peptideDB" value="sample.db"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
135 <conditional name="PSMInputModeCond">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
136 <param name="PSMInputMode" value="single"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
137 <param name="scoredPSMs" value="sample_1.qpsm"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
138 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
139 <param name="ProteinIdentifierRegex" value="id"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
140 <param name="Protein" value="Maximal"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
141 <param name="Peptide" value="Maximal"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
142 <conditional name="GetQValueCond">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
143 <param name="GetQValue" value="Storey"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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144 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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145 <param name="outputParamfile" value="true"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
146 <output name="out_paramfile" file="result_1.json" />
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
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147 </test>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
148 <test expect_num_outputs="2">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
149 <param name="peptideDB" value="sample.db"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
150 <conditional name="PSMInputModeCond">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
151 <param name="PSMInputMode" value="single"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
152 <param name="scoredPSMs" value="sample_1.qpsm"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
153 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
154 <param name="ProteinIdentifierRegex" value="id"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
155 <param name="Protein" value="Minimal"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
156 <param name="Peptide" value="MaximalInverse"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
157 <conditional name="GetQValueCond">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
158 <param name="GetQValue" value="NoQValue"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
159 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
160 <param name="outputParamfile" value="true"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
161 <output name="out_paramfile" file="result_2.json" />
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
162 </test>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
163 <test expect_num_outputs="2">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
164 <param name="peptideDB" value="sample.db"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
165 <conditional name="PSMInputModeCond">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
166 <param name="PSMInputMode" value="single"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
167 <param name="scoredPSMs" value="sample_1.qpsm"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
168 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
169 <param name="ProteinIdentifierRegex" value="id"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
170 <param name="Protein" value="Minimal"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
171 <param name="Peptide" value="MaximalInverse"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
172 <conditional name="GetQValueCond">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
173 <param name="GetQValue" value="LogisticRegression"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
174 <param name="LogisticRegressionType" value="Conservative"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
175 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
176 <param name="outputParamfile" value="true"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
177 <output name="out_paramfile" file="result_3.json" />
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
178 </test>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
179 <test expect_num_outputs="2">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
180 <param name="peptideDB" value="sample.db"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
181 <conditional name="PSMInputModeCond">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
182 <param name="PSMInputMode" value="single"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
183 <param name="scoredPSMs" value="sample_1.qpsm"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
184 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
185 <param name="ProteinIdentifierRegex" value="id"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
186 <param name="Protein" value="Minimal"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
187 <param name="Peptide" value="MaximalInverse"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
188 <conditional name="GetQValueCond">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
189 <param name="GetQValue" value="LogisticRegression"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
190 <param name="LogisticRegressionType" value="MAYU"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
191 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
192 <param name="outputParamfile" value="true"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
193 <output name="out_paramfile" file="result_4.json" />
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
194 </test>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
195 <test expect_num_outputs="2">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
196 <param name="peptideDB" value="sample.db"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
197 <conditional name="PSMInputModeCond">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
198 <param name="PSMInputMode" value="single"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
199 <param name="scoredPSMs" value="sample_1.qpsm"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
200 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
201 <param name="ProteinIdentifierRegex" value="id"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
202 <param name="Protein" value="Minimal"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
203 <param name="Peptide" value="MaximalInverse"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
204 <conditional name="GetQValueCond">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
205 <param name="GetQValue" value="LogisticRegression"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
206 <param name="LogisticRegressionType" value="DecoyTargetRatio"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
207 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
208 <param name="outputParamfile" value="true"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
209 <output name="out_paramfile" file="result_5.json" />
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
210 </test>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
211 <test expect_num_outputs="2">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
212 <param name="peptideDB" value="sample.db"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
213 <conditional name="PSMInputModeCond">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
214 <param name="PSMInputMode" value="multi"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
215 <param name="scoredPSMs" value="sample_1.qpsm,sample_2.qpsm,sample_3.qpsm"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
216 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
217 <param name="ProteinIdentifierRegex" value="id"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
218 <param name="Protein" value="Maximal"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
219 <param name="Peptide" value="Maximal"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
220 <param name="GroupFiles" value="true"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
221 <conditional name="GetQValueCond">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
222 <param name="GetQValue" value="NoQValue"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
223 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
224 <param name="outputParamfile" value="true"/>
1
7729b9043b80 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 6c26a48bade20a6be46dec57602579ffc05cbe27"
galaxyp
parents: 0
diff changeset
225 <output_collection name="out_prot_collection" type="list" count="3" />
0
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
226 <output name="out_paramfile" file="result_6.json" />
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
227 </test>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
228 <test expect_num_outputs="2">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
229 <param name="peptideDB" value="sample.db"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
230 <conditional name="PSMInputModeCond">
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
231 <param name="PSMInputMode" value="multi"/>
1
7729b9043b80 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 6c26a48bade20a6be46dec57602579ffc05cbe27"
galaxyp
parents: 0
diff changeset
232 <param name="scoredPSMs" value="sample_1.qpsm,sample_2.qpsm"/>
0
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233 </conditional>
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234 <param name="ProteinIdentifierRegex" value="id"/>
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235 <param name="Protein" value="Maximal"/>
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236 <param name="Peptide" value="Maximal"/>
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237 <param name="GroupFiles" value="false"/>
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238 <conditional name="GetQValueCond">
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239 <param name="GetQValue" value="NoQValue"/>
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240 </conditional>
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241 <param name="outputParamfile" value="true"/>
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242 <output_collection name="out_prot_collection" type="list" count="2" />
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243 <output name="out_paramfile" file="result_7.json" />
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244 </test>
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245 </tests>
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246 <help>
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247 <![CDATA[
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248 What It Does
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249 ------------
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
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250 **Disclaimer** Disclaimer this tool needs a `peptide database <https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html>`_ and `peptide spectrum matches <https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html>`_ which `passed fdr thresholds <https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html>`_.
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251
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252 MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. This process is not as straightforward as one might think at a first glance on the subject, since the peptide-to-protein mapping is not necessarily a one-to-one relationship but in many cases a one-to-many relationship. This is due to the fact that many proteins share peptides with an identical sequence, e.g. two proteins originating from two different splice variants of the same gene.
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253
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254 One way to cope with this problem is to introduce the concept of protein groups, which allow us to report the aggregation of all peptides which map to all isoforms of a gene independently from the peptides mapping uniquely to a single isoform.
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255 While this approach has its merits it leaves room for fine tuning when implemented.
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256 Lets say we have two proteins pA and pB which were both discovered by one peptide uniquely mapping to each of them and additionally by a third peptide, which maps to both of them: How do we report our findings?
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257 We could report both proteins seperately and as a protein group, we could only report the protein group, or we could report both proteins but not the protein group.
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258 A problem of comparable complexity occurs when we think about peptides when calculating the abundances for the proteingroup pA;pB.
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259 Do we use the peptides only once, or do we also use the peptides mapping uniquely to protein pA and pB?
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260 Fortunately, the tool ProteinInference gives you the possibility to choose any of the described scenarios by tuning the parameters described below.
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261 The following scheme gives an overview how parameter settings influence inferred protein groups:
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262
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263 .. image:: $PATH_TO_IMAGES/ProteinInference.png
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264 :width: 1048pt
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265 :height: 358pt
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266
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267 Moreover, we report each protein group with a so called 'Peptide evidence class'. This metric gives an indication how pure the peptide composition of a protein group is and lets us differentiate between protein groups that consist of isoforms of a splice variant or contain a rather arbitrary mix of proteins.
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268 In order to determine these inter-protein relationships the user can optionally supply a gff3 file.
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269
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270 Further Reading
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271 ---------------
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272 Additional information about the tool can be found in the `documentation <https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html>`_.
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273 ]]>
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274 </help>
1
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275 </tool>