Mercurial > repos > galaxyp > idpqonvert
changeset 2:d239e445e2e6 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 8eadb7632f9240724b853adc997558779bfe7219-dirty
author | galaxyp |
---|---|
date | Thu, 05 Nov 2015 11:54:46 -0500 |
parents | 16cb7537c1a2 |
children | f962717ca1db |
files | idpqonvert.xml |
diffstat | 1 files changed, 20 insertions(+), 20 deletions(-) [+] |
line wrap: on
line diff
--- a/idpqonvert.xml Tue Sep 15 17:50:14 2015 -0400 +++ b/idpqonvert.xml Thu Nov 05 11:54:46 2015 -0500 @@ -19,7 +19,7 @@ <![CDATA[ #set $db_name = $ProteinDatabase.display_name.replace(".fasta", "") + ".fasta" #set $input_name = $input.display_name - #set $output_name = $input_name.split(".")[0] + ".idpDB" + #set $output_name = $input_name.replace(".pep.xml", "").replace(".pepXML", "").replace(".mzid", "") + ".idpDB" ln -s '$input' '${input_name}' && ln -s '$ProteinDatabase' '${db_name}' && @@ -69,17 +69,17 @@ <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" value="0.05" help="PSMs with a greater FDR than this will be excluded from the filtered data set, but remain in the file." /> + <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" 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" value="2" /> - <param argument="-MaxTrainingRank" type="integer" label="Max Training Rank" value="1" /> + <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" value="0.01" /> - <param argument="-PolynomialDegree" type="integer" label="Polynomial Degree" value="3" /> - <param argument="-MinPartitionSize" type="integer" label="Minimum Partition Size" value="10" /> + <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> @@ -120,53 +120,53 @@ </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" value="1" /> + <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" value="1" /> + <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" value="1" /> + <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" value="1" /> + <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" value="1" /> + <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" value="-1" /> + <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" value="1" /> + <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" value="-1" /> + <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" value="1" /> + <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" value="1" /> + <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" value="-1" /> + <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)." value="1" /> + <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>