Mercurial > repos > pieterlukasse > prims_proteomics
changeset 10:72d4a37869ee
updated msfilt/napq interfaces
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Thu, 06 Mar 2014 17:29:19 +0100 |
| parents | cb5d1a3b9aae |
| children | 1a68b939a62e |
| files | msfilt.xml napq.xml |
| diffstat | 2 files changed, 2 insertions(+), 6 deletions(-) [+] |
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--- a/msfilt.xml Thu Mar 06 16:54:09 2014 +0100 +++ b/msfilt.xml Thu Mar 06 17:29:19 2014 +0100 @@ -1,4 +1,4 @@ -<tool name="MsFilt" id="msfilt" version="1.0.2"> +<tool name="MsFilt" id="msfilt" version="1.0.3"> <description>Filters annotations based MS/MS peptide identification and annotation quality measures</description> <!-- For remote debugging start you listener on port 8000 and use the following as command interpreter: @@ -38,8 +38,6 @@ <repeat name="annotationSourceFiles" title="(Optional) Peptide identification files" help="Full set of MS/MS peptide identification files, including peptides that could not be quantified."> <param name="identificationsFile" type="data" format="apml,mzidentml,prims.fileset.zip" label="Identifications file (APML or MZIDENTML or MZIDENTML fileSet)" /> - <param name="spectraFile" type="data" format="mzidentml,prims.fileset.zip" optional="true" label="(Optional) Spectra fileSet (mzml file or fileSet)" - help="Select this in case your Identifications file is MZIDENTML or MZIDENTML fileSet" /> </repeat> <!-- @@ -117,7 +115,7 @@ <configfile name="annotationSourceConfigFile">## start comment ## iterate over the selected files and store their names in the config file #for $i, $s in enumerate( $annotationSourceFiles ) - ${s.identificationsFile}|${s.spectraFile} + ${s.identificationsFile} ## also print out the datatype in the next line, based on previously configured datatype #if isinstance( $s.identificationsFile.datatype, $__app__.datatypes_registry.get_datatype_by_extension('apml').__class__): apml
--- a/napq.xml Thu Mar 06 16:54:09 2014 +0100 +++ b/napq.xml Thu Mar 06 17:29:19 2014 +0100 @@ -22,8 +22,6 @@ <repeat name="identificationFileList" title="Peptide identification files" help="Full set of MS/MS peptide identification files, including peptides that could not be quantified."> <param name="identificationsFile" type="data" format="apml,mzidentml,prims.fileset.zip" label="Identifications file (APML or MZIDENTML or MZIDENTML fileSet)" /> - <param name="spectraFile" type="data" format="mzidentml,prims.fileset.zip" optional="true" label="(Optional) Spectra fileSet (mzml file or fileSet)" - help="Select this in case your Identifications file is MZIDENTML or MZIDENTML fileSet" /> </repeat> <param name="namingConventionCodesForSamples" type="text" size="100" value=""