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comparison bwa-mem.xml @ 6:09a7281d24c5 draft

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planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Tue, 21 Jul 2015 14:12:49 -0400
parents fbf460831036
children d8c9597bfb09
comparison
equal deleted inserted replaced
5:fbf460831036 6:09a7281d24c5
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="bwa_mem" name="Map with BWA-MEM" version="0.3"> 2 <tool id="bwa_mem" name="Map with BWA-MEM" version="0.3.1">
3 <description>- map medium and long reads (&gt; 100 bp) against reference genome</description> 3 <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
4 <macros> 4 <macros>
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 <requirements> 8 <requirements>
9 <requirement type="package" version="0.7.10.039ea20639">bwa</requirement> 9 <requirement type="package" version="0.7.10.039ea20639">bwa</requirement>
10 <requirement type="package" version="1.1">samtools</requirement> 10 <requirement type="package" version="1.1">samtools</requirement>
11 </requirements> 11 </requirements>
12 <stdio> 12 <expand macro="stdio" />
13 <exit_code range="1:" />
14 </stdio>
15 <command> 13 <command>
16 #set $reference_fasta_filename = "localref.fa" 14 #set $reference_fasta_filename = "localref.fa"
17 15
18 #if str( $reference_source.reference_source_selector ) == "history": 16 #if str( $reference_source.reference_source_selector ) == "history":
19 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp; 17 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
289 </when> 287 </when>
290 </conditional> 288 </conditional>
291 </inputs> 289 </inputs>
292 290
293 <outputs> 291 <outputs>
294 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)"/> 292 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
293 <expand macro="dbKeyActionsBwaMem" />
294 </data>
295 </outputs> 295 </outputs>
296 296
297 <tests> 297 <tests>
298 <test> 298 <test>
299 <param name="reference_source_selector" value="history" /> 299 <param name="reference_source_selector" value="history" />