Mercurial > repos > galaxyp > morpheus
changeset 5:f0202024f80b draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999
author | galaxyp |
---|---|
date | Thu, 15 Dec 2016 17:41:38 -0500 |
parents | a7c58067f5ee |
children | 01a572a3a716 |
files | morpheus.xml tool_dependencies.xml |
diffstat | 2 files changed, 34 insertions(+), 38 deletions(-) [+] |
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--- a/morpheus.xml Thu Nov 19 16:13:29 2015 -0500 +++ b/morpheus.xml Thu Dec 15 17:41:38 2016 -0500 @@ -1,4 +1,4 @@ -<tool id="morpheus" name="Morpheus" version="1.171.5"> +<tool id="morpheus" name="Morpheus" version="2.255.0"> <description>database search algorithm for high-resolution tandem mass spectra</description> <macros> <xml name="modification_options"> @@ -41,8 +41,7 @@ </macros> <requirements> - <requirement version="4.0">mono</requirement> - <requirement version="171">morpheus</requirement> + <requirement type="package" version="255">morpheus</requirement> </requirements> <stdio> @@ -54,8 +53,8 @@ </stdio> <command><![CDATA[ - mkdir output_reports; - cwd=`pwd`; + mkdir -p output_reports && + cwd=`pwd` && #import re #set $searchdb_name = $searchdb #if isinstance($searchdb.datatype, $__app__.datatypes_registry.get_datatype_by_extension('uniprotxml').__class__): @@ -75,9 +74,12 @@ && ln -s $input $input_name #end for #set $input_names = ','.join($input_list) - && mono \${MORPHEUS_PATH}/morpheus_cl.exe - -d="$input_names" - -db=$searchdb_name + && + + mono `which morpheus` + -d='$input_names' + -db='$searchdb_name' + #if isinstance($searchdb.datatype, $__app__.datatypes_registry.get_datatype_by_extension('uniprotxml').__class__): #if str( $advanced.adv_options_selector) == "set": $advanced.noup @@ -150,14 +152,16 @@ -vm="$vmods" #end if -mt=\${GALAXY_SLOTS:-4} - #set $out_list = 'summary.tsv PSMs.tsv unique_peptides.tsv protein_groups.tsv log.txt *.pep.xml' - #if len($input_list) > 1: - && ( basepath=`grep 'Proteome Database:' log.txt | sed 's/Proteome Database: \(.*\)${$searchdb_name}/\1/'`; + #set $out_list = 'log.txt summary.tsv aggregate.PSMs.tsv aggregate.unique_peptides.tsv aggregate.protein_groups.tsv aggregate.mzid *.pep.xml' + #if len($input_list) == 1: + && ln -s *.log.txt log.txt + && ln -s *.mzid aggregate.mzid + && ln -s *.unique_peptides.tsv aggregate.unique_peptides.tsv + && ln -s *.protein_groups.tsv aggregate.protein_groups.tsv + && ln -s *.PSMs.tsv aggregate.PSMs.tsv + #end if + && ( basepath=`grep 'Proteome Database:' log.txt | sed 's/Proteome Database: \(.*\)${$searchdb_name}/\1/'`; for i in $out_list; do cat \$i | sed "s#\${basepath}\##" > output_reports/\$i; done ) - #else - && ( basepath=`grep 'Proteome Database:' *.log.txt | head -1 | sed 's/Proteome Database: \(.*\)${$searchdb_name}/\1/'`; - for i in $out_list; do cat *\$i | sed "s#\${basepath}\##" > output_reports/\$i; done ) - #end if ]]></command> <inputs> <param name="inputs" type="data" format="mzml" multiple="true" label='Indexed mzML' /> @@ -223,18 +227,19 @@ </conditional> </inputs> <outputs> + <data name="log" format="txt" label="${tool.name} on ${on_string}: log.txt" from_work_dir="output_reports/log.txt" /> <data name="summary" format="txt" label="${tool.name} on ${on_string}: summary.tsv" from_work_dir="output_reports/summary.tsv" /> - <data name="log" format="txt" label="${tool.name} on ${on_string}: log.txt" from_work_dir="output_reports/log.txt" /> - <data name="output_psms" format="tabular" label="${tool.name} on ${on_string}: PSMs.tsv" from_work_dir="output_reports/PSMs.tsv" /> - <data name="output_unique_peptides" format="tabular" label="${tool.name} on ${on_string}: unique_peptides.tsv" from_work_dir="output_reports/unique_peptides.tsv" /> - <data name="output_protein_groups" format="tabular" label="${tool.name} on ${on_string}: protein_groups.tsv" from_work_dir="output_reports/protein_groups.tsv" /> + <data name="output_psms" format="tabular" label="${tool.name} on ${on_string}: PSMs.tsv" from_work_dir="output_reports/aggregate.PSMs.tsv" /> + <data name="output_unique_peptides" format="tabular" label="${tool.name} on ${on_string}: unique_peptides.tsv" from_work_dir="output_reports/aggregate.unique_peptides.tsv" /> + <data name="output_protein_groups" format="tabular" label="${tool.name} on ${on_string}: protein_groups.tsv" from_work_dir="output_reports/aggregate.protein_groups.tsv" /> + <data name="aggregate_mzid" format="mzid" label="${tool.name} on ${on_string}: aggregate.mzid" from_work_dir="output_reports/aggregate.mzid" /> <collection name="morpheus_pep_xmls" type="list" label="${tool.name} on ${on_string} pep.xml"> - <discover_datasets pattern="(?P<name>.*\.pep.xml)" ext="pepxml" visible="False" directory="output_reports" /> + <discover_datasets pattern="(?P<name>.*\.pep.xml)" ext="pepxml" visible="false" directory="output_reports" /> </collection> </outputs> <tests> <test> - <param name="input" value="test_input.mzML" ftype="mzml"/> + <param name="inputs" value="test_input.mzML" ftype="mzml"/> <param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/> <param name="fdr" value="1"/> <param name="mvmi" value="1024"/> @@ -243,14 +248,14 @@ <param name="precmtv" value="2.5"/> <output name="output_psms"> <assert_contents> - <has_text text="K.TTGSSSSSSSK.K" /> - <not_has_text text="carbamidomethylation of C" /> - <not_has_text text="(oxidation of M)" /> + <not_has_text text="K.TTGSSSSSSSK.K" /> + <has_text text="carbamidomethylation of C" /> + <has_text text="(oxidation of M)" /> </assert_contents> </output> </test> <test> - <param name="input" value="test_input.mzML" ftype="mzml"/> + <param name="inputs" value="test_input.mzML" ftype="mzml"/> <param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/> <param name="fdr" value="1"/> <param name="mvmi" value="1024"/> @@ -267,7 +272,7 @@ </output> </test> <test> - <param name="input" value="test_input.mzML" ftype="mzml"/> + <param name="inputs" value="test_input.mzML" ftype="mzml"/> <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/> <param name="fdr" value="1"/> <param name="mvmi" value="1024"/> @@ -284,7 +289,7 @@ </output> </test> <test> - <param name="input" value="test_input.mzML" ftype="mzml"/> + <param name="inputs" value="test_input.mzML" ftype="mzml"/> <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/> <param name="fdr" value="1"/> <param name="mvmi" value="1024"/> @@ -297,8 +302,8 @@ <param name="prodmtv" value=".01"/> <output name="output_psms"> <assert_contents> - <has_text text="K.KYFLENKIGTDR.R" /> - <not_has_text text="R.KRSLFDS(UniProt: Phosphoserine)AFSSR.A" /> + <has_text text="K.KTLKSDGVAGLYR.G" /> + <not_has_text text="K.RSPSGNISTNSMR.P" /> </assert_contents> </output> </test>
--- a/tool_dependencies.xml Thu Nov 19 16:13:29 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="mono" version="4.0"> - <repository changeset_revision="d081ac7d12d1" name="package_mono_4_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="morpheus" version="171"> - <repository changeset_revision="a8e9d3b708f2" name="package_morpheus_171" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>