| Previous changeset 0:445a02a846f3 (2019-03-23) |
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Commit message:
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mixcr commit d027d2142cfcd0169c5c24f9bea63dd2d6cfe887-dirty |
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modified:
mixcr_analyze.xml |
| b |
| diff -r 445a02a846f3 -r b112efe1994a mixcr_analyze.xml --- a/mixcr_analyze.xml Sat Mar 23 20:56:38 2019 -0400 +++ b/mixcr_analyze.xml Tue Mar 26 13:01:34 2019 -0400 |
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| @@ -5,17 +5,24 @@ </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ + #import os.path + #import re + #def clean(name) + #set $base_name = $os.path.basename($name) + #set $name_clean = re.sub('[^\w\-_\.]', '_', $base_name) + #return $name_clean + #end def #if $imgt.library_selector == 'history': - #set $libname = $imgt.library.name + #set $libname = $re.sub('.gz$','',$clean($imgt.library.name)) ln -s -f $imgt.library $libname && #end if #if str( $fastq_input.fastq_input_selector ) == "paired": - #set $fq1 = $fastq_input.fastq_input1.name + #set $fq1 = $clean($fastq_input.fastq_input1.name) ln -s -f $fastq_input.fastq_input1 $fq1 && - #set $fq2 = $fastq_input.fastq_input2.name + #set $fq2 = $clean($fastq_input.fastq_input2.name) ln -s -f $fastq_input.fastq_input2 $fq2 && #else: - #set $fq1 = $fastq_input.fastq_input1.name + #set $fq1 = $clean($fastq_input.fastq_input1.name) ln -s -f $fastq_input.fastq_input1 $fq1 && #end if mixcr analyze $analyze.pipeline --starting-material $starting_material |