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comparison mixcr_analyze.xml @ 1:b112efe1994a draft default tip

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mixcr commit d027d2142cfcd0169c5c24f9bea63dd2d6cfe887-dirty
author jjohnson
date Tue, 26 Mar 2019 13:01:34 -0400
parents 445a02a846f3
children
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0:445a02a846f3 1:b112efe1994a
3 <macros> 3 <macros>
4 <import>mixcr_macros.xml</import> 4 <import>mixcr_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #import os.path
9 #import re
10 #def clean(name)
11 #set $base_name = $os.path.basename($name)
12 #set $name_clean = re.sub('[^\w\-_\.]', '_', $base_name)
13 #return $name_clean
14 #end def
8 #if $imgt.library_selector == 'history': 15 #if $imgt.library_selector == 'history':
9 #set $libname = $imgt.library.name 16 #set $libname = $re.sub('.gz$','',$clean($imgt.library.name))
10 ln -s -f $imgt.library $libname && 17 ln -s -f $imgt.library $libname &&
11 #end if 18 #end if
12 #if str( $fastq_input.fastq_input_selector ) == "paired": 19 #if str( $fastq_input.fastq_input_selector ) == "paired":
13 #set $fq1 = $fastq_input.fastq_input1.name 20 #set $fq1 = $clean($fastq_input.fastq_input1.name)
14 ln -s -f $fastq_input.fastq_input1 $fq1 && 21 ln -s -f $fastq_input.fastq_input1 $fq1 &&
15 #set $fq2 = $fastq_input.fastq_input2.name 22 #set $fq2 = $clean($fastq_input.fastq_input2.name)
16 ln -s -f $fastq_input.fastq_input2 $fq2 && 23 ln -s -f $fastq_input.fastq_input2 $fq2 &&
17 #else: 24 #else:
18 #set $fq1 = $fastq_input.fastq_input1.name 25 #set $fq1 = $clean($fastq_input.fastq_input1.name)
19 ln -s -f $fastq_input.fastq_input1 $fq1 && 26 ln -s -f $fastq_input.fastq_input1 $fq1 &&
20 #end if 27 #end if
21 mixcr analyze $analyze.pipeline --starting-material $starting_material 28 mixcr analyze $analyze.pipeline --starting-material $starting_material
22 #if $analyze.pipeline == 'amplicon': 29 #if $analyze.pipeline == 'amplicon':
23 --5-end $analyze.primers5end 30 --5-end $analyze.primers5end