Mercurial > repos > iuc > samtools_fixmate

comparison samtools_fixmate.xml @ 1:77af4d28aca3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:31:39 -0400
parents 47c0cf039aae
children bc77b4b67147
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0:47c0cf039aae 1:77af4d28aca3
9 <command><![CDATA[ 9 <command><![CDATA[
10 @ADDTHREADS@ 10 @ADDTHREADS@
11 ## name sort input 11 ## name sort input
12 #if not $bamfile.is_of_type('qname_sorted.bam', 'qnamed_input_sorted.bam'): 12 #if not $bamfile.is_of_type('qname_sorted.bam', 'qnamed_input_sorted.bam'):
13 samtools sort 13 samtools sort
14 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp 14 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
15 -n 15 -n
16 -O BAM 16 -O BAM
17 -o namesorted.bam 17 -o namesorted.bam
18 '$bamfile' && 18 '$bamfile' &&
19 #else: 19 #else: