Mercurial > repos > iuc > bwa_mem2
comparison bwa-mem2.xml @ 2:b4a22d90cce9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 563c0931e9fc14b0d6e8a7d64ad042a483ec9bb4"
author | iuc |
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date | Wed, 24 Nov 2021 21:29:45 +0000 |
parents | 82217dccdbcf |
children | bfaa0d22c2e4 |
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1:88bcfaea2fb6 | 2:b4a22d90cce9 |
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3 <macros> | 3 <macros> |
4 <import>read_group_macros.xml</import> | 4 <import>read_group_macros.xml</import> |
5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
8 <expand macro="xrefs"/> | |
8 <expand macro="stdio"/> | 9 <expand macro="stdio"/> |
9 <expand macro="xrefs"/> | |
10 <command><![CDATA[ | 10 <command><![CDATA[ |
11 @pipefail@ | 11 @pipefail@ |
12 @set_reference_fasta_filename@ | 12 @set_reference_fasta_filename@ |
13 | 13 |
14 ## Begin BWA-MEM command line | 14 ## Begin BWA-MEM command line |
304 <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="4" /> | 304 <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="4" /> |
305 </test> | 305 </test> |
306 <test> | 306 <test> |
307 <param name="reference_source_selector" value="history" /> | 307 <param name="reference_source_selector" value="history" /> |
308 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> | 308 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
309 <param name="index_a" value="is"/> | |
310 <param name="fastq_input_selector" value="paired"/> | 309 <param name="fastq_input_selector" value="paired"/> |
311 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> | 310 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> |
312 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> | 311 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> |
313 <param name="rg_selector" value="set"/> | 312 <param name="rg_selector" value="set"/> |
314 <param name="ID" value="rg1"/> | 313 <param name="ID" value="rg1"/> |