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comparison bwa-mem.xml @ 20:4f774c1e6049 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 4a306ebd8b7808ce963a69a3b15dd860c1fde585
author iuc
date Thu, 01 Feb 2018 12:35:35 -0500
parents 48f306c57611
children 8d2a528a9513
comparison
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19:dfd8b7f78c37 20:4f774c1e6049
5 <import>read_group_macros.xml</import> 5 <import>read_group_macros.xml</import>
6 <import>bwa_macros.xml</import> 6 <import>bwa_macros.xml</import>
7 </macros> 7 </macros>
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
9 <expand macro="stdio"/> 9 <expand macro="stdio"/>
10 <command> 10 <command><![CDATA[
11 <![CDATA[
12 @set_reference_fasta_filename@ 11 @set_reference_fasta_filename@
13 12
14 ## Begin BWA-MEM command line 13 ## Begin BWA-MEM command line
15 14
16 bwa mem 15 bwa mem
105 '${reference_fasta_filename}' 104 '${reference_fasta_filename}'
106 '${fastq_input.fastq_input1}' 105 '${fastq_input.fastq_input1}'
107 #end if 106 #end if
108 107
109 | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$bam_output' 108 | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$bam_output'
110 ]]> 109 ]]></command>
111 </command>
112 110
113 <inputs> 111 <inputs>
114 <expand macro="reference_source_conditional" /> 112 <expand macro="reference_source_conditional" />
115 <conditional name="fastq_input"> 113 <conditional name="fastq_input">
116 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> 114 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">