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comparison lofreq_call.xml @ 6:e1461b5c52a0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit c1fda24943cf04866d408133ffb6aabf4a90866b"
author iuc
date Mon, 05 Oct 2020 20:14:06 +0000
parents 65432c3abf6c
children 4805fe3d8fda
comparison
equal deleted inserted replaced
5:65432c3abf6c 6:e1461b5c52a0
1 <tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy1" profile="18.01">
2 <description>with LoFreq</description> 2 <description>with LoFreq</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
32 #set $ign_vcfs = ','.join($ign_vcfs) 32 #set $ign_vcfs = ','.join($ign_vcfs)
33 #end if 33 #end if
34 34
35 ## call variants with lofreq 35 ## call variants with lofreq
36 36
37 ## make lofreq stick to tool contract by
38 ## generating tmp output inside job working dir
39 mkdir pp-tmp &&
40 export TMPDIR=pp-tmp &&
41
42 lofreq call-parallel --pp-threads \${GALAXY_SLOTS:-1} --verbose 37 lofreq call-parallel --pp-threads \${GALAXY_SLOTS:-1} --verbose
43 38
44 --ref '$reference_fasta_fn' --out variants.vcf $variant_types 39 --ref '$reference_fasta_fn' --out variants.vcf $variant_types
45 40
46 #if str($regions.restrict_to_region) == 'regions_from_file': 41 #if str($regions.restrict_to_region) == 'regions_from_file':
94 89
95 reads.bam 2>&1 90 reads.bam 2>&1
96 91
97 ## in case of errors add the log files produced 92 ## in case of errors add the log files produced
98 ## by the parallel workers to stderr 93 ## by the parallel workers to stderr
99 || (tool_exit_code=\$? && cat pp-tmp/lofreq2_call_parallel*/*.log 1>&2 && exit \$tool_exit_code) 94 || (tool_exit_code=\$? && cat "\$TMPDIR/lofreq2_call_parallel*/*.log" 1>&2 && exit \$tool_exit_code)
100 95
101 ## work around a bug in lofreq call-parallel 96 ## work around a bug in lofreq call-parallel
102 ## https://github.com/CSB5/lofreq/issues/85 97 ## https://github.com/CSB5/lofreq/issues/85
103 ## that causes the output format to be vcf.gz with certain filter 98 ## that causes the output format to be vcf.gz with certain filter
104 ## combinations. 99 ## combinations. Issue is closed but still not fixed.
105 #if str($bonf_factor) != 'dynamic': 100 #if str($bonf_factor) != 'dynamic':
106 #if '--no-default-filter' in str($filter_control.others): 101 #if '--no-default-filter' in str($filter_control.others):
107 && ln -s variants.vcf variants.vcf.gz 102 && ln -s variants.vcf variants.vcf.gz
108 && gzip -df variants.vcf.gz 103 && gzip -df variants.vcf.gz
109 #end if 104 #end if