Mercurial > repos > devteam > bwa
comparison bwa-mem.xml @ 20:4f774c1e6049 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 4a306ebd8b7808ce963a69a3b15dd860c1fde585
author | iuc |
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date | Thu, 01 Feb 2018 12:35:35 -0500 |
parents | 48f306c57611 |
children | 8d2a528a9513 |
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19:dfd8b7f78c37 | 20:4f774c1e6049 |
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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"> |