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comparison samtools_calmd.xml @ 3:3d873744df7e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
author iuc
date Mon, 29 Jul 2019 08:47:41 -0400
parents e65c2cd0964c
children 06dc50b7b711
comparison
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2:e65c2cd0964c 3:3d873744df7e
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 #if str( $reference_source.reference_source_selector ) == "history": 10 @ADDTHREADS@
11 #set ref_fa = 'ref.fa' 11 #if str( $reference_source.reference_source_selector ) == "history":
12 ln -s '${reference_source.ref_fasta}' ref.fa && 12 #set ref_fa = 'ref.fa'
13 samtools faidx ref.fa && 13 ln -s '${reference_source.ref_fasta}' ref.fa &&
14 #else: 14 samtools faidx ref.fa &&
15 #set ref_fa = str( $reference_source.ref_fasta.fields.path ) 15 #else:
16 #end if 16 #set ref_fa = str( $reference_source.ref_fasta.fields.path )
17 #end if
17 18
18 samtools calmd 19 samtools calmd
19 $baq_settings.use_baq $baq_settings.modify_quality $baq_settings.extended_baq 20 $baq_settings.use_baq $baq_settings.modify_quality $baq_settings.extended_baq
20 #if str($option_set.option_sets) == 'advanced': 21 #if str($option_set.option_sets) == 'advanced':
21 $option_set.change_identical -C $option_set.adjust_mq 22 $option_set.change_identical -C $option_set.adjust_mq
22 #end if 23 #end if
23 -b 24 -b
24 '$input_bam' 25 -@ \$addthreads
25 '$ref_fa' 26 '$input_bam'
26 > '$calmd_output' 27 '$ref_fa'
28 > '$calmd_output'
27 ]]></command> 29 ]]></command>
28 <inputs> 30 <inputs>
29 <param name="input_bam" type="data" format="bam" label="BAM file to recalculate" /> 31 <param name="input_bam" type="data" format="bam" label="BAM file to recalculate" />
30 <conditional name="reference_source"> 32 <conditional name="reference_source">
31 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> 33 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">