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comparison msfilt.xml @ 10:72d4a37869ee

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updated msfilt/napq interfaces
author pieter.lukasse@wur.nl
date Thu, 06 Mar 2014 17:29:19 +0100
parents d50f079096ee
children 40ec8770780d
comparison
equal deleted inserted replaced
9:cb5d1a3b9aae 10:72d4a37869ee
1 <tool name="MsFilt" id="msfilt" version="1.0.2"> 1 <tool name="MsFilt" id="msfilt" version="1.0.3">
2 <description>Filters annotations based MS/MS peptide identification and annotation quality measures</description> 2 <description>Filters annotations based MS/MS peptide identification and annotation quality measures</description>
3 <!-- 3 <!--
4 For remote debugging start you listener on port 8000 and use the following as command interpreter: 4 For remote debugging start you listener on port 8000 and use the following as command interpreter:
5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
6 ////////////////////////// 6 //////////////////////////
36 help="The APML contents as aligned and annotated feature lists. E.g. produced by 36 help="The APML contents as aligned and annotated feature lists. E.g. produced by
37 SEDMAT or Quantiline tools." /> 37 SEDMAT or Quantiline tools." />
38 38
39 <repeat name="annotationSourceFiles" title="(Optional) Peptide identification files" help="Full set of MS/MS peptide identification files, including peptides that could not be quantified."> 39 <repeat name="annotationSourceFiles" title="(Optional) Peptide identification files" help="Full set of MS/MS peptide identification files, including peptides that could not be quantified.">
40 <param name="identificationsFile" type="data" format="apml,mzidentml,prims.fileset.zip" label="Identifications file (APML or MZIDENTML or MZIDENTML fileSet)" /> 40 <param name="identificationsFile" type="data" format="apml,mzidentml,prims.fileset.zip" label="Identifications file (APML or MZIDENTML or MZIDENTML fileSet)" />
41 <param name="spectraFile" type="data" format="mzidentml,prims.fileset.zip" optional="true" label="(Optional) Spectra fileSet (mzml file or fileSet)"
42 help="Select this in case your Identifications file is MZIDENTML or MZIDENTML fileSet" />
43 </repeat> 41 </repeat>
44 42
45 <!-- 43 <!--
46 <param name="maxNrRankings" type="integer" size="10" value="0" label="Maximum nr. of items to leave in the final ranking (set=0 for no limit) " /> 44 <param name="maxNrRankings" type="integer" size="10" value="0" label="Maximum nr. of items to leave in the final ranking (set=0 for no limit) " />
47 --> 45 -->
115 <configfile name="rankingMetadataFile">${rankingWeightConfig}</configfile> 113 <configfile name="rankingMetadataFile">${rankingWeightConfig}</configfile>
116 <configfile name="statisticalMeasuresConfigFile">${statisticalMeasuresConfig}</configfile> 114 <configfile name="statisticalMeasuresConfigFile">${statisticalMeasuresConfig}</configfile>
117 <configfile name="annotationSourceConfigFile">## start comment 115 <configfile name="annotationSourceConfigFile">## start comment
118 ## iterate over the selected files and store their names in the config file 116 ## iterate over the selected files and store their names in the config file
119 #for $i, $s in enumerate( $annotationSourceFiles ) 117 #for $i, $s in enumerate( $annotationSourceFiles )
120 ${s.identificationsFile}|${s.spectraFile} 118 ${s.identificationsFile}
121 ## also print out the datatype in the next line, based on previously configured datatype 119 ## also print out the datatype in the next line, based on previously configured datatype
122 #if isinstance( $s.identificationsFile.datatype, $__app__.datatypes_registry.get_datatype_by_extension('apml').__class__): 120 #if isinstance( $s.identificationsFile.datatype, $__app__.datatypes_registry.get_datatype_by_extension('apml').__class__):
123 apml 121 apml
124 #else: 122 #else:
125 mzid 123 mzid