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comparison samtools_stats.xml @ 5:5a08c09b9311 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
author iuc
date Mon, 29 Jul 2019 08:49:54 -0400
parents 793ad847121d
children 47035d167365
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4:793ad847121d 5:5a08c09b9311
8 <requirement type="package" version="5.26">perl</requirement> 8 <requirement type="package" version="5.26">perl</requirement>
9 </expand> 9 </expand>
10 <expand macro="stdio"/> 10 <expand macro="stdio"/>
11 <expand macro="version_command"/> 11 <expand macro="version_command"/>
12 <command><![CDATA[ 12 <command><![CDATA[
13 @ADDTHREADS@
13 @PREPARE_IDX@ 14 @PREPARE_IDX@
14 @PREPARE_FASTA_IDX@ 15 @PREPARE_FASTA_IDX@
15 samtools stats 16 samtools stats
16 #if $coverage_cond.coverage_select == 'yes': 17 #if $coverage_cond.coverage_select == 'yes':
17 --coverage ${coverage_cond.coverage_min},${coverage_cond.coverage_max},${coverage_cond.coverage_step} 18 --coverage ${coverage_cond.coverage_min},${coverage_cond.coverage_max},${coverage_cond.coverage_step}
63 @REGIONS_FILE@ 64 @REGIONS_FILE@
64 $remove_overlaps 65 $remove_overlaps
65 #if str($cov_threshold): 66 #if str($cov_threshold):
66 -g $cov_threshold 67 -g $cov_threshold
67 #end if 68 #end if
69 -@ \$addthreads
68 infile 70 infile
69 @REGIONS_MANUAL@ 71 @REGIONS_MANUAL@
70 > '$output' 72 > '$output'
71 73
72 #if $cond_plot.select_plot=='yes': 74 #if $cond_plot.select_plot=='yes':