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comparison snippy.xml @ 10:0c9f91faff96 draft

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Added zippeed output folder as an output for use in snippy core.
author simon-gladman
date Wed, 08 Jun 2016 09:56:14 -0400
parents 234020dc16f7
children 68a43b0593a3
comparison
equal deleted inserted replaced
9:234020dc16f7 10:0c9f91faff96
1 <tool id="snippy" name="snippy" version="0.3"> 1 <tool id="snippy" name="snippy" version="0.2.0">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="3.0">snippy</requirement> 3 <requirement type="package" version="3.0">snippy</requirement>
4 </requirements> 4 </requirements>
5 <stdio> 5 <stdio>
6 <exit_code range="1:" /> 6 <exit_code range="1:" />
50 #end if 50 #end if
51 51
52 && 52 &&
53 53
54 gunzip out/snps.depth.gz 54 gunzip out/snps.depth.gz
55
56 &&
57
58 bgzip -c out > out.bgz
55 59
56 60
57 ]]></command> 61 ]]></command>
58 <inputs> 62 <inputs>
59 <conditional name="reftype"> 63 <conditional name="reftype">
117 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa"/> 121 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa"/>
118 <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth"/> 122 <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth"/>
119 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam"> 123 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
120 <filter>cleanup is False</filter> 124 <filter>cleanup is False</filter>
121 </data> 125 </data>
126 <data format="bgzip" name="outdir" label="${tool.name} on ${on_string} out dir" from_work_dir="out.bgz" />
122 </outputs> 127 </outputs>
123 128
124 <tests> 129 <tests>
125 <test> 130 <test>
126 <param name="ref_type_selector" value="fasta" /> 131 <param name="ref_type_selector" value="fasta" />