Mercurial > repos > galaxyp > proteomiqon_proteininference

annotate proteomiqon_proteininference.xml @ 0:8e4fb95a319a draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
author galaxyp
date Mon, 26 Jul 2021 13:34:26 +0000
parents
children 7729b9043b80
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0
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.
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4 </description>
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5 <macros>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
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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[
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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 #elif $PSMInputModeCond.PSMInputMode == "multi"
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17 #for $psmfile in $PSMInputModeCond.scoredPSMs
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18 #set basename = $re.sub(r'[^\w ,.\-+]','_',$psmfile.element_identifier)
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19 ln -s '$psmfile' '${basename}.qpsm' &&
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20 #end for
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21 #end if
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22 #if $outputParamfile:
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23 cat '$paramfile' >> '$out_paramfile' &&
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24 #end if
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25 proteomiqon-proteininference -i './' -d '$peptideDB' -p '$paramfile' -o './out'
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26 ]]>
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27 </command>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
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28 <configfiles>
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29 <configfile name="paramfile">
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30 <![CDATA[
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
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31 {
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
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32 "ProteinIdentifierRegex": "${ProteinIdentifierRegex}",
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33 "Protein": {
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34 "Case": "${Protein}"
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35 },
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36 "Peptide": {
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37 "Case": "${Peptide}"
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38 },
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39 "GroupFiles": ${GroupFiles},
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40 #if $GetQValueCond.GetQValue == "LogisticRegression"
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41 "GetQValue": {
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42 "Case": "${GetQValueCond.GetQValue}",
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43 "Fields": [
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44 {
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
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45 "Case": "${GetQValueCond.LogisticRegressionType}"
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46 }
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47 ]
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48 }
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49 #else
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50 "GetQValue": {
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51 "Case": "${GetQValueCond.GetQValue}",
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52 }
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53 #end if
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54 }
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55 ]]>
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56 </configfile>
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57 </configfiles>
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58 <inputs>
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59 <param name="peptideDB" type="data" format="sqlite" label="Peptide database" help="Specify the peptide data base."/>
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60 <conditional name="PSMInputModeCond">
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61 <param name="PSMInputMode" type="select" label="PSM file input mode">
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62 <option value="single">Single File</option>
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63 <option value="multi">Multiple Files</option>
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64 </param>
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65 <when value="single">
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66 <param name="scoredPSMs" type="data" format="tabular" label="Scored PSM file" help="Specify peptide identifications." />
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67 </when>
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68 <when value="multi">
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69 <param name="scoredPSMs" type="data" format="tabular" label="Scored PSM files" help="Specify list of peptide identifications." multiple="true"/>
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70 </when>
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71 </conditional>
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72 <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.">
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73 <sanitizer sanitize="false" />
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74 </param>
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75 <param name="Protein" type="select" label="Protein" help="Specify how protein groups are created. For details please refer to the description below.">
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76 <option value="Minimal">Minimal</option>
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77 <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
78 </param>
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="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
80 <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
81 <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
82 <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
83 </param>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
84 <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."/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
85 <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
86 <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
87 <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
88 <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
89 <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
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 <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
92 <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
93 <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:
diff changeset
94 <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:
diff changeset
95 <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:
diff changeset
96 <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:
diff changeset
97 </param>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
98 </when>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
99 <when value="NoQValue"/>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
100 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
101 <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:
diff changeset
102 </inputs>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
103 <outputs>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
104 <data format="tabular" name="out_prot" >
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
105 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.prot" ext="tabular" directory="out" visible="true" assign_primary_output="true" />
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
106 </data>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
107 <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
parents:
diff changeset
108 <filter>outputParamfile</filter>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
109 </data>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
110 </outputs>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
111 <tests>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
112 <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
113 <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
114 <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
115 <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
116 <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
117 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
118 <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
119 <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
120 <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
121 <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
122 <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
123 </test>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
124 <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
125 <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
126 <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
127 <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
128 <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
129 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
130 <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
131 <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
132 <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
133 <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
134 <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
135 <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:
diff changeset
136 </conditional>
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="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
138 <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:
diff changeset
139 </test>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
140 <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
141 <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
142 <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
143 <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
144 <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
145 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
146 <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
147 <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
148 <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
149 <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
150 <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
151 <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
152 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
153 <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
154 <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
155 </test>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
156 <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
157 <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
158 <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
159 <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
160 <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
161 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
162 <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
163 <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
164 <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
165 <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
166 <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
167 <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
168 <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
169 </conditional>
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="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
171 <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
172 </test>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
173 <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
174 <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
175 <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
176 <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
177 <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
178 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
179 <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
180 <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
181 <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
182 <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
183 <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
184 <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
185 <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
186 </conditional>
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="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
188 <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
189 </test>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
190 <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
191 <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
192 <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
193 <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
194 <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
195 </conditional>
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="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
197 <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
198 <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
199 <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
200 <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
201 <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
202 <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
203 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
204 <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
205 <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
206 </test>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
207 <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
208 <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
209 <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
210 <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
211 <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
212 </conditional>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
213 <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
214 <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
215 <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
216 <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
217 <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
218 <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
219 </conditional>
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="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
221 <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
222 </test>
8e4fb95a319a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 1b4c15d5c84c890663475a22cc6ff71bbc9aa90c"
galaxyp
parents:
diff changeset
223 <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
224 <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
225 <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
226 <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
227 <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
228 </conditional>
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="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
230 <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
231 <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:
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232 <param name="GroupFiles" value="false"/>
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233 <conditional name="GetQValueCond">
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234 <param name="GetQValue" value="NoQValue"/>
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235 </conditional>
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236 <param name="outputParamfile" value="true"/>
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237 <output name="out_paramfile" file="result_7.json" />
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238 </test>
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239 </tests>
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240 <help>
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241 <![CDATA[
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242 What It Does
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243 ------------
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244 **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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245
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246 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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247
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248 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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249 While this approach has its merits it leaves room for fine tuning when implemented.
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250 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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251 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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252 A problem of comparable complexity occurs when we think about peptides when calculating the abundances for the proteingroup pA;pB.
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253 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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254 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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255 The following scheme gives an overview how parameter settings influence inferred protein groups:
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256
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257 .. image:: $PATH_TO_IMAGES/ProteinInference.png
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258 :width: 1048pt
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259 :height: 358pt
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260
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261 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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262 In order to determine these inter-protein relationships the user can optionally supply a gff3 file.
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263
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264 Further Reading
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265 ---------------
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266 Additional information about the tool can be found in the `documentation <https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html>`_.
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267 ]]>
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268 </help>
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269 </tool>