Mercurial > repos > galaxyp > proteomiqon_proteininference
changeset 1:7729b9043b80 draft default tip
"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 |
| children | |
| files | proteomiqon_proteininference.xml test-data/result_1.json test-data/result_2.json test-data/result_3.json test-data/result_4.json test-data/result_5.json |
| diffstat | 6 files changed, 22 insertions(+), 16 deletions(-) [+] |
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--- a/proteomiqon_proteininference.xml Mon Jul 26 13:34:26 2021 +0000 +++ b/proteomiqon_proteininference.xml Fri Apr 29 19:29:14 2022 +0000 @@ -13,6 +13,8 @@ #if $PSMInputModeCond.PSMInputMode == "single" #set basename = $re.sub(r'[^\w ,.\-+]','_',$PSMInputModeCond.scoredPSMs.element_identifier) ln -s '$scoredPSMs' '${basename}.qpsm' && + mkdir './out' && + ln -s '$out_prot' './out/${basename}.prot' && #elif $PSMInputModeCond.PSMInputMode == "multi" #for $psmfile in $PSMInputModeCond.scoredPSMs #set basename = $re.sub(r'[^\w ,.\-+]','_',$psmfile.element_identifier) @@ -36,7 +38,11 @@ "Peptide": { "Case": "${Peptide}" }, - "GroupFiles": ${GroupFiles}, + #if $PSMInputModeCond.PSMInputMode == "multi" + "GroupFiles": ${PSMInputModeCond.GroupFiles}, + #else + "GroupFiles": false, + #end if #if $GetQValueCond.GetQValue == "LogisticRegression" "GetQValue": { "Case": "${GetQValueCond.GetQValue}", @@ -67,6 +73,7 @@ </when> <when value="multi"> <param name="scoredPSMs" type="data" format="tabular" label="Scored PSM files" help="Specify list of peptide identifications." multiple="true"/> + <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."/> </when> </conditional> <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."> @@ -81,7 +88,6 @@ <option value="Maximal">Maximal</option> <option value="MaximalInverse">MaximalInverse</option> </param> - <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."/> <conditional name="GetQValueCond"> <param name="GetQValue" type="select" label="Q-Value method" help="Specify if and how q-value calculation should be carried out."> <option value="Storey" selected="true">Storey</option> @@ -102,8 +108,12 @@ </inputs> <outputs> <data format="tabular" name="out_prot" > - <discover_datasets pattern="(?P<designation>.+)\.prot" ext="tabular" directory="out" visible="true" assign_primary_output="true" /> + <filter>PSMInputModeCond['PSMInputMode'] == 'single'</filter> </data> + <collection type="list" format="tabular" name="out_prot_collection" > + <discover_datasets pattern="(?P<designation>.+\.prot)" directory="out" /> + <filter>PSMInputModeCond['PSMInputMode'] == 'multi'</filter> + </collection> <data format="json" name="out_paramfile"> <filter>outputParamfile</filter> </data> @@ -118,7 +128,6 @@ <param name="ProteinIdentifierRegex" value="id"/> <param name="Protein" value="Minimal"/> <param name="Peptide" value="Minimal"/> - <param name="GroupFiles" value="true"/> <param name="outputParamfile" value="false"/> </test> <test expect_num_outputs="2"> @@ -130,7 +139,6 @@ <param name="ProteinIdentifierRegex" value="id"/> <param name="Protein" value="Maximal"/> <param name="Peptide" value="Maximal"/> - <param name="GroupFiles" value="true"/> <conditional name="GetQValueCond"> <param name="GetQValue" value="Storey"/> </conditional> @@ -146,7 +154,6 @@ <param name="ProteinIdentifierRegex" value="id"/> <param name="Protein" value="Minimal"/> <param name="Peptide" value="MaximalInverse"/> - <param name="GroupFiles" value="true"/> <conditional name="GetQValueCond"> <param name="GetQValue" value="NoQValue"/> </conditional> @@ -162,7 +169,6 @@ <param name="ProteinIdentifierRegex" value="id"/> <param name="Protein" value="Minimal"/> <param name="Peptide" value="MaximalInverse"/> - <param name="GroupFiles" value="true"/> <conditional name="GetQValueCond"> <param name="GetQValue" value="LogisticRegression"/> <param name="LogisticRegressionType" value="Conservative"/> @@ -179,7 +185,6 @@ <param name="ProteinIdentifierRegex" value="id"/> <param name="Protein" value="Minimal"/> <param name="Peptide" value="MaximalInverse"/> - <param name="GroupFiles" value="true"/> <conditional name="GetQValueCond"> <param name="GetQValue" value="LogisticRegression"/> <param name="LogisticRegressionType" value="MAYU"/> @@ -196,7 +201,6 @@ <param name="ProteinIdentifierRegex" value="id"/> <param name="Protein" value="Minimal"/> <param name="Peptide" value="MaximalInverse"/> - <param name="GroupFiles" value="true"/> <conditional name="GetQValueCond"> <param name="GetQValue" value="LogisticRegression"/> <param name="LogisticRegressionType" value="DecoyTargetRatio"/> @@ -218,13 +222,14 @@ <param name="GetQValue" value="NoQValue"/> </conditional> <param name="outputParamfile" value="true"/> + <output_collection name="out_prot_collection" type="list" count="3" /> <output name="out_paramfile" file="result_6.json" /> </test> <test expect_num_outputs="2"> <param name="peptideDB" value="sample.db"/> <conditional name="PSMInputModeCond"> <param name="PSMInputMode" value="multi"/> - <param name="scoredPSMs" value="sample_1.qpsm,sample_2.qpsm,sample_3.qpsm"/> + <param name="scoredPSMs" value="sample_1.qpsm,sample_2.qpsm"/> </conditional> <param name="ProteinIdentifierRegex" value="id"/> <param name="Protein" value="Maximal"/> @@ -234,6 +239,7 @@ <param name="GetQValue" value="NoQValue"/> </conditional> <param name="outputParamfile" value="true"/> + <output_collection name="out_prot_collection" type="list" count="2" /> <output name="out_paramfile" file="result_7.json" /> </test> </tests> @@ -266,4 +272,4 @@ Additional information about the tool can be found in the `documentation <https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html>`_. ]]> </help> -</tool> \ No newline at end of file +</tool>
--- a/test-data/result_1.json Mon Jul 26 13:34:26 2021 +0000 +++ b/test-data/result_1.json Fri Apr 29 19:29:14 2022 +0000 @@ -8,7 +8,7 @@ "Peptide": { "Case": "Maximal" }, - "GroupFiles": true, + "GroupFiles": false, "GetQValue": { "Case": "Storey", }
--- a/test-data/result_2.json Mon Jul 26 13:34:26 2021 +0000 +++ b/test-data/result_2.json Fri Apr 29 19:29:14 2022 +0000 @@ -8,7 +8,7 @@ "Peptide": { "Case": "MaximalInverse" }, - "GroupFiles": true, + "GroupFiles": false, "GetQValue": { "Case": "NoQValue", }
--- a/test-data/result_3.json Mon Jul 26 13:34:26 2021 +0000 +++ b/test-data/result_3.json Fri Apr 29 19:29:14 2022 +0000 @@ -8,7 +8,7 @@ "Peptide": { "Case": "MaximalInverse" }, - "GroupFiles": true, + "GroupFiles": false, "GetQValue": { "Case": "LogisticRegression", "Fields": [