Mercurial > repos > pieterlukasse > prims_proteomics

comparison napq.xml @ 16:d56c18ed0f77

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fix in comment and in configuration
author pieter.lukasse@wur.nl
date Fri, 28 Mar 2014 14:43:46 +0100
parents 72d4a37869ee
children 40ec8770780d
comparison
equal deleted inserted replaced
15:33962926e260 16:d56c18ed0f77
18 -outReportPicturesPath $htmlReportFile.files_path 18 -outReportPicturesPath $htmlReportFile.files_path
19 </command> 19 </command>
20 20
21 <inputs> 21 <inputs>
22 22
23 <repeat name="identificationFileList" title="Peptide identification files" help="Full set of MS/MS peptide identification files, including peptides that could not be quantified."> 23 <repeat name="identificationFileList" title="Peptide identification files" help="Set of MS/MS peptide identification files that have some form of quantification data coupled to it (e.g. MSE identifications&amp;intensity).">
24 <param name="identificationsFile" type="data" format="apml,mzidentml,prims.fileset.zip" label="Identifications file (APML or MZIDENTML or MZIDENTML fileSet)" /> 24 <param name="identificationsFile" type="data" format="apml,mzidentml,prims.fileset.zip" label="Identifications file (APML or MZIDENTML or MZIDENTML fileSet)" />
25 </repeat> 25 </repeat>
26 26
27 <param name="namingConventionCodesForSamples" type="text" size="100" value="" 27 <param name="namingConventionCodesForSamples" type="text" size="100" value=""
28 label="Part of run/file name that identifies the sample" 28 label="Part of run/file name that identifies the sample"
48 </inputs> 48 </inputs>
49 <configfiles> 49 <configfiles>
50 <configfile name="identificationsConfigFile">## start comment 50 <configfile name="identificationsConfigFile">## start comment
51 ## iterate over the selected files and store their names in the config file 51 ## iterate over the selected files and store their names in the config file
52 #for $i, $s in enumerate( $identificationFileList ) 52 #for $i, $s in enumerate( $identificationFileList )
53 ${s.identificationsFile}|${s.spectraFile} 53 ${s.identificationsFile}
54 ## also print out the datatype in the next line, based on previously configured datatype 54 ## also print out the datatype in the next line, based on previously configured datatype
55 #if isinstance( $s.identificationsFile.datatype, $__app__.datatypes_registry.get_datatype_by_extension('apml').__class__): 55 #if isinstance( $s.identificationsFile.datatype, $__app__.datatypes_registry.get_datatype_by_extension('apml').__class__):
56 apml 56 apml
57 #else: 57 #else:
58 mzid 58 mzid