Mercurial > repos > iuc > multiqc

comparison multiqc.xml @ 5:5746cb5cf08d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 36465d526cea3d061724952bb6cf63ee8dd069bf
author iuc
date Tue, 05 Dec 2017 05:24:03 -0500
parents e4574a4d09d8
children 01237d721a9f
comparison
equal deleted inserted replaced
4:e4574a4d09d8 5:5746cb5cf08d
1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.0"> 1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.1">
2 <description>aggregate results from bioinformatics analyses into a single report</description> 2 <description>aggregate results from bioinformatics analyses into a single report</description>
3 <macros> 3 <macros>
4 <token name="@WRAPPER_VERSION@">1.2</token> 4 <token name="@WRAPPER_VERSION@">1.2</token>
5 <token name="@LN_FILES@"> 5 <token name="@LN_FILES@">
6 <![CDATA[ 6 <![CDATA[
105 #end if 105 #end if
106 #end for 106 #end for
107 #elif str($repeat.software_cond.software) == "featureCounts" 107 #elif str($repeat.software_cond.software) == "featureCounts"
108 #for $file in $repeat.software_cond.input 108 #for $file in $repeat.software_cond.input
109 #set file_prefix = $software_dir + '/' + str($file.element_identifier) 109 #set file_prefix = $software_dir + '/' + str($file.element_identifier)
110 #if $file.metadata.column_names and $file.metadata.column_names.find(',') != -1 110 if grep -qw Status '$file'; then
111 echo '$file.metadata.column_names.replace(',','\t').replace('__ob__u','').replace('u__sq__','').replace('__sq__','').replace('__cb__','')' >> '${file_prefix}.summary' && 111 ln -s '$file' '${file_prefix}.summary';
112 cat '$file' >> '${file_prefix}.summary' && 112 else
113 #else 113 echo -e 'Status\t$file.element_identifier' > '${file_prefix}.summary';
114 ln -s '$file' '${file_prefix}.summary' && 114 cat '$file' >> '${file_prefix}.summary';
115 #end if 115 fi &&
116 #end for 116 #end for
117 #elif str($repeat.software_cond.software) == "flexbar" 117 #elif str($repeat.software_cond.software) == "flexbar"
118 #set $pattern = "flexible barcode and adapter removal" 118 #set $pattern = "flexible barcode and adapter removal"
119 @LN_FILES@ 119 @LN_FILES@
120 #elif str($repeat.software_cond.software) == "gatk" 120 #elif str($repeat.software_cond.software) == "gatk"