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comparison samtools_stats.xml @ 6:e37d8a076d91 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty
author iuc
date Sun, 28 Jul 2019 14:50:47 -0400
parents fd4f3d13e501
children 896a72e79738
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5:fd4f3d13e501 6:e37d8a076d91
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':