Mercurial > repos > iuc > multiqc
comparison multiqc.xml @ 5:5746cb5cf08d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 36465d526cea3d061724952bb6cf63ee8dd069bf
author | iuc |
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date | Tue, 05 Dec 2017 05:24:03 -0500 |
parents | e4574a4d09d8 |
children | 01237d721a9f |
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4:e4574a4d09d8 | 5:5746cb5cf08d |
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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" |