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comparison samtools_fastx.xml @ 2:af994f4458bc draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:31:10 -0400
parents a5429e2e18e8
children c933a9166b1d
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1:a5429e2e18e8 2:af994f4458bc
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command><![CDATA[ 9 <command><![CDATA[
10 @ADDTHREADS@ 10 @ADDTHREADS@
11 ## name sort input file if neccessary 11 ## name sort input file if neccessary
12 #if not $input.is_of_type('qname_sorted.bam', 'qname_input_sorted.bam'): 12 #if not $input.is_of_type('qname_sorted.bam', 'qname_input_sorted.bam'):
13 samtools sort -@ \$addthreads -n '$input' > input && 13 samtools sort -@ \$addthreads -n '$input' -T "\${TMPDIR:-.}" > input &&
14 #else: 14 #else:
15 ln -s '$input' input && 15 ln -s '$input' input &&
16 #end if 16 #end if
17 17
18 #set command=str($output_fmt_cond.output_fmt_select)[:5] 18 #set command=str($output_fmt_cond.output_fmt_select)[:5]