Mercurial > repos > galaxyp > morpheus
diff morpheus.xml @ 1:ecb9ec15083d draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999
| author | galaxyp |
|---|---|
| date | Thu, 15 Dec 2016 17:41:50 -0500 |
| parents | 553f0336e43e |
| children | e0104a9f20f0 |
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--- a/morpheus.xml Mon May 23 09:51:47 2016 -0400 +++ b/morpheus.xml Thu Dec 15 17:41:50 2016 -0500 @@ -41,8 +41,7 @@ </macros> <requirements> - <requirement version="4.0">mono</requirement> - <requirement version="255">morpheus</requirement> + <requirement type="package" version="255">morpheus</requirement> </requirements> <stdio> @@ -55,7 +54,7 @@ <command><![CDATA[ mkdir -p output_reports && - cwd=`pwd`&& + 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_mzml_mono_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": $advanced.noup @@ -232,12 +234,12 @@ <data name="output_protein_groups" format="tabular" label="${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"/> @@ -246,14 +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"/> @@ -270,7 +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"/> @@ -287,7 +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"/>