Mercurial > repos > iuc > lofreq_call

comparison lofreq_call.xml @ 8:3116e6e4a934 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 814935de92514901b397ad335e9a43dba728973f
author iuc
date Wed, 02 Oct 2024 08:19:36 +0000
parents 66345032017a
children
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7:66345032017a 8:3116e6e4a934
1 <tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy2" profile="18.01"> 1 <tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy3" 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" />
89 89
90 reads.bam 2>&1 90 reads.bam 2>&1
91 91
92 ## in case of errors add the log files produced 92 ## in case of errors add the log files produced
93 ## by the parallel workers to stderr 93 ## by the parallel workers to stderr
94 || (tool_exit_code=\$? && cat "\$TMPDIR/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)
95 95
96 ## work around a bug in lofreq call-parallel 96 ## work around a bug in lofreq call-parallel
97 ## https://github.com/CSB5/lofreq/issues/85 97 ## https://github.com/CSB5/lofreq/issues/85
98 ## 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
99 ## combinations. Issue is closed but still not fixed. 99 ## combinations. Issue is closed but still not fixed.