Mercurial > repos > peterjc > mira_assembler

comparison tools/mira_3_4/mira.xml @ 7:e810e45bdad7 draft

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Uploaded v0.0.8, first attempt at unit test. Known to fail on local Galaxy install, suspected to be a test framework limitation.
author peterjc
date Tue, 30 Apr 2013 11:42:07 -0400
parents 1e49ca6731cd
children da604cc07658
comparison
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6:1e49ca6731cd 7:e810e45bdad7
1 <tool id="mira_assembler" name="Assemble with MIRA" version="0.0.6"> 1 <tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.8">
2 <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description> 2 <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
3 <requirements> 3 <requirements>
4 <requirement type="python-module">Bio</requirement> 4 <requirement type="python-module">Bio</requirement>
5 <requirement type="binary">mira</requirement> 5 <requirement type="binary">mira</requirement>
6 <requirement type="package" version="3.4.1.1">MIRA</requirement> 6 <requirement type="package" version="3.4.1.1">MIRA</requirement>
137 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" /> 137 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
138 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" /> 138 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
139 <data name="out_log" format="txt" label="MIRA log" /> 139 <data name="out_log" format="txt" label="MIRA log" />
140 </outputs> 140 </outputs>
141 <tests> 141 <tests>
142 <test>
143 <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses
144 strain data and miraSearchESTSNPs. Here we just assemble it. -->
145 <param name="job_method" value="denovo" />
146 <param name="job_type" value="est" />
147 <param name="job_qual" value="accurate" />
148 <param name="condBackbone.use" value="false" />
149 <param name="condSanger.use" value="true" />
150 <param name="condSanger.filename" value="tvc_mini.fastq" ftype="fastq" />
151 <param name="condRoche.use" value="false" />
152 <param name="condIllumina.use" value="false" />
153 <param name="condIonTorrent.use" value="false" />
154 <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
155 </test>
142 </tests> 156 </tests>
143 <help> 157 <help>
144 158
145 **What it does** 159 **What it does**
146 160