Mercurial > repos > galaxyp > dia_umpire
changeset 1:acd0df26c1e9 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 73496bb9686e60f25d1cccf3410f1c53bf92d5f5-dirty
author | galaxyp |
---|---|
date | Wed, 24 Jan 2018 08:08:58 -0500 |
parents | e8f7be6a6e59 |
children | b4f82d15cac0 |
files | dia_umpire_se.xml |
diffstat | 1 files changed, 17 insertions(+), 13 deletions(-) [+] |
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--- a/dia_umpire_se.xml Tue Jan 23 14:45:50 2018 -0500 +++ b/dia_umpire_se.xml Wed Jan 24 08:08:58 2018 -0500 @@ -22,17 +22,20 @@ && echo " " >> $se_params && echo "Thread = \$GALAXY_SLOTS" >> $se_params #if $input_prefix and len($input_prefix.strip()) > 0: -#set $input_path = $ser_dir + "/" + $input_prefix.__str__ + "_rep" + str($i + 1) + ".mzXML" +#set $input_path = str($output_dir) + '/' + $input_prefix.__str__ + '_rep' + str($i + 1) + '.mzXML' #else: -#set $input_path = $ser_dir + "/" + $re.sub('\.[mM]\w+$','',$re.sub('[^-a-zA-Z0-9_.]','_',$input.name)) + ".mzXML" +#set $input_path = str($output_dir) + '/' + $re.sub('\.[mM]\w+$','',$re.sub('[^-a-zA-Z0-9_.]','_',$input.name)) + '.mzXML' #end if && ln -s '${input}' '$input_path' && dia_umpire_se '$input_path' '$se_params' && cat $output_dir/*.log >> "$logfile" #if not $mgfs_as_collection: -&& cp '$output_dir/*_Q1.mgf' '$q1_mgf' -&& cp '$output_dir/*_Q2.mgf' '$q2_mgf' -&& cp '$output_dir/*_Q3.mgf' '$q3_mgf' +&& cp "$output_dir/"*_Q1.mgf '$q1_mgf' +&& cp "$output_dir/"*_Q2.mgf '$q2_mgf' +&& cp "$output_dir/"*_Q3.mgf '$q3_mgf' +#end if +#if $ExportPrecursorPeak: +&& cp "$output_dir/"*PeakCluster.csv '$PrecursorPeak' #end if ]]> </command> @@ -392,7 +395,7 @@ <param name="ExportFragmentPeak" type="boolean" truevalue="true" falsevalue="false" checked="false" label="ExportFragmentPeak" help="Output detailed information about detected MS2 signals"/> - <param name="se_extraction_data" type="boolean" truevalue="true" falsevalue="false" checked="false" + <param name="se_extraction_data" type="boolean" truevalue="Signal Extraction data" falsevalue="diaumpire_se.params" checked="false" label="Output Signal Extraction data for DIA_Umpire_Quant" /> <param name="mgfs_as_collection" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output MGFs as a collection" /> @@ -400,27 +403,28 @@ </inputs> <outputs> - <data format="txt" name="logfile" label="${tool.name} log"/> - <data format="dia_umpire.ser" name="se_params" label="${tool.name} Signal Extraction data"> - <filter>se_extraction_data</filter> + <data format="txt" name="logfile" label="${tool.name} ${on_string} log"/> + <data format="dia_umpire.ser" name="se_params" label="${tool.name} ${input.name} ${se_extraction_data}"> </data> - <data format="csv" name="PrecursorPeak" label="" from_work_dir="gx_path/swath_PeakCurve.csv"> + <data format="csv" name="PrecursorPeak" label="${tool.name} ${input.name} PeakCluster.csv" from_work_dir="gx_path/swath_PeakCurve.csv"> <filter>ExportPrecursorPeak</filter> </data> + <!-- <data format="csv" name="FragmentPeak" label="" from_work_dir="gx_path/swath_PeakCurve.csv"> <filter>ExportFragmentPeak</filter> </data> + --> <collection name="dia_umpire_se_mgfs" type="list" label="${tool.name} MGFs"> <filter>mgfs_as_collection</filter> <discover_datasets pattern="(?P<name>.*Q[1-3]\.mgf)" ext="mgf" visible="false" directory="gx_path" /> </collection> - <data format="csv" name="q1_mgf" label="${tool.name} Q1.mgf" > + <data format="mgf" name="q1_mgf" label="${tool.name} ${input.name}_Q1.mgf" > <filter>not mgfs_as_collection</filter> </data> - <data format="csv" name="q2_mgf" label="${tool.name} Q2.mgf" > + <data format="mgf" name="q2_mgf" label="${tool.name} ${input.name}_Q2.mgf" > <filter>not mgfs_as_collection</filter> </data> - <data format="csv" name="q3_mgf" label="${tool.name} Q3.mgf" > + <data format="mgf" name="q3_mgf" label="${tool.name} ${input.name}_Q3.mgf" > <filter>not mgfs_as_collection</filter> </data> </outputs>