Mercurial > repos > galaxyp > idpqonvert
diff idpqonvert.xml @ 3:d1f7b2395bc2 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
| author | galaxyp |
|---|---|
| date | Thu, 15 Dec 2016 17:20:57 -0500 |
| parents | |
| children | feebe32c3a52 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/idpqonvert.xml Thu Dec 15 17:20:57 2016 -0500 @@ -0,0 +1,207 @@ +<?xml version="1.0"?> +<tool id="idpqonvert" name="idpQonvert" version="@VERSION@.0"> + <description>Prepare identification results for IDPicker</description> + <macros> + <import>macros.xml</import> + <xml name="normalizationOptions"> + <option value="off" selected="true">None</option> + <option value="quantile">Quantile</option> + <option value="linear">Linear</option> + </xml> + </macros> + <expand macro="requirements" /> + <stdio> + <exit_code range="1:" level="fatal" description="Job Failed" /> + <regex match="^Error:.*$" source="both" level="fatal" /> + </stdio> + <command> +<![CDATA[ + #set $db_name = $ProteinDatabase.display_name.replace(".fasta", "") + ".fasta" + #set $input_name = $input.display_name + #set $output_name = $input_name.split(".")[0] + ".idpDB" + ln -s '$input' '${input_name}' && + ln -s '$ProteinDatabase' '${db_name}' && + + idpQonvert + -DecoyPrefix '${DecoyPrefix}' + -WriteQonversionDetails true + -ProteinDatabase '${db_name}' + -MaxFDR $MaxFDR + -EmbedSpectrumScanTimes false + -EmbedSpectrumSources false + #set $score_info = [] + #for $engine in ["myrimatch:mvh", "xcorr", "sequest:xcorr", "sequest:deltacn", "mascot:score", "x!tandem:expect", "x!tandem:hyperscore", "ms-gf:specevalue", "comet:xcorr", "comet:deltacn", "comet:expect"] + #set $name = $engine.replace(":", "_").replace("!","") + #set $weight = $getVar("scoring." + $name + "." + $name + "_weight.value") + #set $type = $getVar("scoring." + $name + "." + $name + "_type.value") + #set $score_info = $score_info + [str($weight) + " " + $type + " " + $engine] + #continue + #end for + #for $i, $s in enumerate($scoring.extra_score) + #set $name = $s.extra_score_name + #set $type = $s.extra_score_normalization + #set $weight = $s.extra_score_weight + #set $score_info = $score_info + [str($weight) + " " + $type + " " + $name] + #end for + #set $score_str = "; ".join($score_info) + -ScoreInfo '$score_str' + -MaxImportFDR $advanced_options.MaxImportFDR + -MaxResultRank $advanced_options.MaxResultRank + -RerankMatches $advanced_options.RerankMatches + -Gamma $advanced_options.Gamma + -Nu $advanced_options.Nu + -PolynomialDegree $advanced_options.PolynomialDegree + -TruePositiveThreshold $advanced_options.TruePositiveThreshold + -MaxTrainingRank $advanced_options.MaxTrainingRank + -SVMType $advanced_options.SVMType + -Kernel $advanced_options.Kernel + -ChargeStateHandling $advanced_options.ChargeStateHandling + -TerminalSpecificityHandling $advanced_options.TerminalSpecificityHandling + -MissedCleavagesHandling $advanced_options.MissedCleavagesHandling + -QonverterMethod $advanced_options.QonverterMethod + -MinPartitionSize $advanced_options.MinPartitionSize + '${input_name}' && + mv '$output_name' output +]]> + </command> + <inputs> + <param name="input" type="data" format="mzid,raw_pepxml" label="Input mzIdentML/pepXML file(s)" /> + <param argument="-ProteinDatabase" format="fasta" type="data" label="Protein Database" help="The FASTA protein database to map peptides against. Only peptides from target proteins will be mapped; decoy peptides will be stored as-is in the idpDB." /> + <param argument="-DecoyPrefix" type="text" label="Decoy Prefix" help="The prefix to look for on protein accessions to determine whether it is a target or decoy." /> + <param argument="-MaxFDR" type="float" label="Max FDR" min="0.0000001" value="0.05" help="PSMs with a greater FDR than this will be excluded from the filtered data set, but remain in the file." /> + <section name="advanced_options" title="Advanced Options"> + <param argument="-MaxImportFDR" type="float" label="Max Import FDR" min="0.1" value="0.25" help="PSMs with a greater FDR than this will be completely excluded from the idpDB." /> + <param argument="-MaxResultRank" type="integer" label="Max Result Rank" min="1" value="2" /> + <param argument="-MaxTrainingRank" type="integer" label="Max Training Rank" min="1" value="1" /> + <param argument="-RerankMatches" type="boolean" label="Rerank Matches" checked="false" truevalue="true" falsevalue="false" /> + <param argument="-Gamma" type="float" label="Gamma" value="5" /> + <param argument="-Nu" type="float" label="Nu" value="-0.5" /> + <param argument="-TruePositiveThreshold" type="float" label="True Positive Threshold" min="0.0000001" value="0.01" /> + <param argument="-PolynomialDegree" type="integer" label="Polynomial Degree" min="1" value="3" /> + <param argument="-MinPartitionSize" type="integer" label="Minimum Partition Size" min="10" value="10" /> + <param argument="-SVMType" label="SVM Type" type="select"> + <option value="CSVC" selected="true">CSVC</option> + <option value="NuSVC">Nu SCV</option> + <option value="OneClass">One Class</option> + <option value="NuSVR">Nu SVR</option> + <option value="EpsilonSVR">Epsilon SVR</option> + </param> + <param argument="-Kernel" label="Kernel" type="select"> + <option value="Linear" selected="true">Linear</option> + <option value="Polynomial">Polynomial</option> + <option value="RBR">Radial Basis Function</option> + <option value="Sigmoid">Sigmoid</option> + </param> + <param argument="-ChargeStateHandling" label="Charge State Handling" type="select"> + <option value="Partition" selected="true">Partition</option> + <option value="Ignore">Ignore</option> + <option value="Feature">Feature</option> + </param> + <param argument="-TerminalSpecificityHandling" label="Terminal Specificity Handling" type="select"> + <option value="Partition" selected="true">Partition</option> + <option value="Ignore">Ignore</option> + <option value="Feature">Feature</option> + </param> + <param argument="-MissedCleavagesHandling" label="Missed Cleavages Handling" type="select"> + <option value="Ignore" selected="true">Ignore</option> + <option value="Feature">Feature</option> + </param> + <param argument="-MassErrorHandling" label="Mass Error Handling" type="select"> + <option value="Ignore" selected="true">Ignore</option> + <option value="Feature">Feature</option> + </param> + <param argument="-QonverterMethod" label="Qonverter Method" type="select"> + <option value="MonteCarlo" selected="true">Monte Carlo (recommended)</option> + <option value="SingleSVM">SVM (single)</option> + <option value="PartitionSVM">SVM (parition)</option> + <option value="StaticWeighted">Static Weighted</option> + </param> + </section> + <section name="scoring" title="Custom Score Settings"> + <section name="myrimatch_mvh" title="Myrimatch (mvh) Score/Weight" expanded="False"> + <param name="myrimatch_mvh_weight" label="Myrimatch (mvh) Weight" type="float" min="-1" max="1" value="1" /> + <param name="myrimatch_mvh_type" label="Myrimatch (mvh) Normalization" type="select"><expand macro="normalizationOptions" /></param> + </section> + <section name="xcorr" title="Non-Sequest (xcorr) Score/Weight" expanded="False"> + <param name="xcorr_weight" label="XCorr Weight" type="float" min="-1" max="1" value="1" /> + <param name="xcorr_type" label="XCorr Normalization" type="select"><expand macro="normalizationOptions" /></param> + </section> + <section name="sequest_xcorr" title="Sequest (xcorr) Score/Weight" expanded="False"> + <param name="sequest_xcorr_weight" label="Sequest (xcorr) Weight" type="float" min="-1" max="1" value="1" /> + <param name="sequest_xcorr_type" label="Sequest (xcorr) Normalization" type="select"><expand macro="normalizationOptions" /></param> + </section> + <section name="sequest_deltacn" title="Sequest (deltacn) Score/Weight" expanded="False"> + <param name="sequest_deltacn_weight" label="Sequest (deltacn) Weight" type="float" min="-1" max="1" value="1" /> + <param name="sequest_deltacn_type" label="Sequest (deltacn) Normalization" type="select"><expand macro="normalizationOptions" /></param> + </section> + <section name="mascot_score" title="Mascot (score) Score/Weight" expanded="False"> + <param name="mascot_score_weight" label="Mascot Score Weight" type="float" min="-1" max="1" value="1" /> + <param name="mascot_score_type" label="Mascot Score Normalization" type="select"><expand macro="normalizationOptions" /></param> + </section> + <section name="xtandem_expect" title="X! Tandem (expect) Score/Weight" expanded="False"> + <param name="xtandem_expect_weight" label="X! Tandem (expectation) Weight" type="float" min="-1" max="1" value="-1" /> + <param name="xtandem_expect_type" label="X! Tandem (expectation) Normalization" type="select"><expand macro="normalizationOptions" /></param> + </section> + <section name="xtandem_hyperscore" title="X! Tandem (hyperscore) Score/Weight" expanded="False"> + <param name="xtandem_hyperscore_weight" label="X! Tandem (hyperscore) Weight" type="float" min="-1" max="1" value="1" /> + <param name="xtandem_hyperscore_type" label="X! Tandem (hyperscore)Normalization" type="select"><expand macro="normalizationOptions" /></param> + </section> + <section name="ms-gf_specevalue" title="MS-GF+ (specevalue) Score/Weight" expanded="False"> + <param name="ms-gf_specevalue_weight" label="MS-GF+ (specevalue) Weight" type="float" min="-1" max="1" value="-1" /> + <param name="ms-gf_specevalue_type" label="MS-GF+ (specevalue) Normalization" type="select"><expand macro="normalizationOptions" /></param> + </section> + <section name="comet_xcorr" title="Comet (xcorr) Score/Weight" expanded="False"> + <param name="comet_xcorr_weight" label="Comet (xcorr) Weight" type="float" min="-1" max="1" value="1" /> + <param name="comet_xcorr_type" label="Comet (xcorr) Normalization" type="select"><expand macro="normalizationOptions" /></param> + </section> + <section name="comet_deltacn" title="Comet (deltacn) Score/Weight" expanded="False"> + <param name="comet_deltacn_weight" label="Comet (deltacn) Weight" type="float" min="-1" max="1" value="1" /> + <param name="comet_deltacn_type" label="Comet (deltacn) Normalization" type="select"><expand macro="normalizationOptions" /></param> + </section> + <section name="comet_expect" title="Comet (expect) Score/Weight" expanded="False"> + <param name="comet_expect_weight" label="Comet (expect) Weight" type="float" min="-1" max="1" value="-1" /> + <param name="comet_expect_type" label="Comet (expect) Normalization" type="select"><expand macro="normalizationOptions" /></param> + </section> + <repeat name="extra_score" title="Extra Search Engine Score/Weight"> + <param name="extra_score_name" label="Name" type="text" help="For scores in the PSI-MS controlled vocabulary, this field must match the name for that score; for other scores, the UserParam name or pepXML name will suffice." value="SearchEngineName" /> + <param name="extra_score_normalization" label="Normalization Method" type="select"><expand macro="normalizationOptions" /></param> + <param name="extra_score_weight" label="Weight" type="float" help="Negative weights indicate that a lower score is better (e.g. expectation value, p-value)." min="-1" max="1" value="1" /> + </repeat> + </section> + </inputs> + <outputs> + <data format="idpdb" name="output" from_work_dir="output" /> + </outputs> + <tests> + <test> + <param name="input" value="input/201208-378803-myrimatch.pepXML" /> + <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" /> + <param name="MaxFDR" value="0.05" /> + <output name="output" file="201208-378803-myrimatch.idpDB" compare="sim_size" delta="500000" /> + </test> + <test> + <param name="input" value="input/201208-378803-cm.pep.xml" /> + <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" /> + <param name="MaxFDR" value="0.05" /> + <output name="output" file="201208-378803-cm.idpDB" compare="sim_size" delta="500000" /> + </test> + <test> + <param name="input" value="input/201208-378803-msgf.mzid" /> + <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" /> + <param name="MaxFDR" value="0.05" /> + <output name="output" file="201208-378803-msgf.idpDB" compare="sim_size" delta="500000" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +Creates IDPicker 3 idpDB files from pepXML and mzIdentML files. The input files should be unfiltered and must come from a target/decoy database search. +]]> + </help> + <citations> + <citation type="doi">10.1021/pr900360j</citation> + <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, + year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" --> + </citations> +</tool>