Mercurial > repos > peterjc > mira_assembler

comparison tools/mira_3_4/mira.xml @ 9:5573d802e431 draft

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Uploaded v0.0.8, MIT licence, RST for README, citation information, development moved to GitHub.
author peterjc
date Wed, 18 Sep 2013 06:22:19 -0400
parents 4266cccbb45a
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8:4266cccbb45a 9:5573d802e431
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 <version_command interpreter="python">mira.py -v</version_command> 3 <requirements>
4 <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log 4 <requirement type="python-module">Bio</requirement>
5 <requirement type="binary">mira</requirement>
6 <requirement type="package" version="3.4.1.1">MIRA</requirement>
7 </requirements>
8 <version_command interpreter="python">mira.py -v</version_command>
9 <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
5 ##Give the wrapper script list of output filenames, then the mira command... 10 ##Give the wrapper script list of output filenames, then the mira command...
6 mira --job=$job_method,$job_type,$job_quality 11 mira --job=$job_method,$job_type,$job_quality
7 12
8 ##Input files 13 ##Input files
9 #if $condBackbone.use == "true": 14 #if $condBackbone.use == "true":
50 55
51 ##put mira temp directory on local storage 56 ##put mira temp directory on local storage
52 -DI:trt=/tmp 57 -DI:trt=/tmp
53 58
54 </command> 59 </command>
55 <inputs> 60 <inputs>
56 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)"> 61 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
57 <option value="denovo">De novo</option> 62 <option value="denovo">De novo</option>
58 <option value="mapping">Mapping</option> 63 <option value="mapping">Mapping</option>
59 </param> 64 </param>
60 <param name="job_type" type="select" label="Assembly type"> 65 <param name="job_type" type="select" label="Assembly type">
122 <when value="true"> 127 <when value="true">
123 <!-- TODO? Support SFF files directly, e.g. with sff_extract --> 128 <!-- TODO? Support SFF files directly, e.g. with sff_extract -->
124 <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" /> 129 <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
125 </when> 130 </when>
126 </conditional> 131 </conditional>
127 </inputs> 132 </inputs>
128 <outputs> 133 <outputs>
129 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" /> 134 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
130 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" /> 135 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" />
131 <data name="out_caf" format="txt" label="MIRA contigs (CAF)" /> 136 <data name="out_caf" format="txt" label="MIRA contigs (CAF)" />
132 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" /> 137 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
133 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" /> 138 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
134 <data name="out_log" format="txt" label="MIRA log" /> 139 <data name="out_log" format="txt" label="MIRA log" />
135 </outputs> 140 </outputs>
136 <tests> 141 <tests>
137 </tests> 142 <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses
138 <requirements> 143 strain data and miraSearchESTSNPs. Here we just assemble it. -->
139 <requirement type="python-module">Bio</requirement> 144 <!--
140 <requirement type="binary">mira</requirement> 145 Commenting out test until Galaxy framework is fixed,
141 </requirements> 146 https://trello.com/c/zSTrfDOB/820-disambiguated-conditional-parameters-not-supported-in-unit-tests
142 <help> 147 <test>
148 <param name="job_method" value="denovo" />
149 <param name="job_type" value="est" />
150 <param name="job_qual" value="accurate" />
151 <param name="condBackbone.use" value="false" />
152 <param name="condSanger.use" value="true" />
153 <param name="condSanger.filename" value="tvc_mini.fastq" ftype="fastq" />
154 <param name="condRoche.use" value="false" />
155 <param name="condIllumina.use" value="false" />
156 <param name="condIonTorrent.use" value="false" />
157 <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
158 </test>
159 -->
160 </tests>
161 <help>
143 162
144 **What it does** 163 **What it does**
145 164
146 Runs MIRA v3.4, collects the output, and throws away all the temporary files. 165 Runs MIRA v3.4, collects the output, and throws away all the temporary files.
147 166
167 MIRA is an open source assembly tool capable of handling sequence data from
168 a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454 and also
169 Ion Torrent).
170
171 It is particularly suited to small genomes such as bacteria.
172
148 **Citation** 173 **Citation**
149 174
150 If you use this tool in scientific work leading to a publication, please cite: 175 If you use this Galaxy tool in work leading to a scientific publication please
176 cite the following papers:
151 177
152 Chevreux et al. (1999) Genome Sequence Assembly Using Trace Signals and Additional Sequence Information Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56. 178 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
179 Galaxy tools and workflows for sequence analysis with applications
180 in molecular plant pathology. PeerJ 1:e167
181 http://dx.doi.org/10.7717/peerj.167
153 182
154 </help> 183 Chevreux et al. (1999).
184 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
185 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
186
187 This wrapper is available to install into other Galaxy Instances via the Galaxy
188 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
189
190 </help>
155 </tool> 191 </tool>