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comparison bwa.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
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5:fbf460831036 6:09a7281d24c5
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="bwa" name="Map with BWA" version="0.3.0"> 2 <tool id="bwa" name="Map with BWA" version="0.3.1">
3 <description>- map short reads (&lt; 100 bp) against reference genome</description> 3 <description>- map short reads (&lt; 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 <token name="@command_options@"> 7 <token name="@command_options@">
68 68
69 <requirements> 69 <requirements>
70 <requirement type="package" version="0.7.10.039ea20639">bwa</requirement> 70 <requirement type="package" version="0.7.10.039ea20639">bwa</requirement>
71 <requirement type="package" version="1.1">samtools</requirement> 71 <requirement type="package" version="1.1">samtools</requirement>
72 </requirements> 72 </requirements>
73 <stdio> 73 <expand macro="stdio" />
74 <exit_code range="1:" />
75 </stdio>
76 <command> 74 <command>
77 #set $reference_fasta_filename = "localref.fa" 75 #set $reference_fasta_filename = "localref.fa"
78 76
79 #if str( $reference_source.reference_source_selector ) == "history": 77 #if str( $reference_source.reference_source_selector ) == "history":
80 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp; 78 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
369 </when> 367 </when>
370 </conditional> 368 </conditional>
371 </inputs> 369 </inputs>
372 370
373 <outputs> 371 <outputs>
374 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)"/> 372 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
373 <expand macro="dbKeyActionsBwa" />
374 </data>
375 </outputs> 375 </outputs>
376 376
377 <tests> 377 <tests>
378 <test> 378 <test>
379 <param name="reference_source_selector" value="history" /> 379 <param name="reference_source_selector" value="history" />