Mercurial > repos > peterjc > mira_assembler

comparison tools/mira_3_4/mira.xml @ 9:b1d60b46d282 draft

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Uploaded v0.0.8 take 3, citation information added, commented out test
author peterjc
date Wed, 11 Sep 2013 06:21:44 -0400
parents da604cc07658
children 84cb67beb1ea
comparison
equal deleted inserted replaced
8:da604cc07658 9:b1d60b46d282
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 142 <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses
144 strain data and miraSearchESTSNPs. Here we just assemble it. --> 143 strain data and miraSearchESTSNPs. Here we just assemble it. -->
144 <!--
145 Commenting out test until Galaxy framework is fixed,
146 https://trello.com/c/zSTrfDOB/820-disambiguated-conditional-parameters-not-supported-in-unit-tests
147 <test>
145 <param name="job_method" value="denovo" /> 148 <param name="job_method" value="denovo" />
146 <param name="job_type" value="est" /> 149 <param name="job_type" value="est" />
147 <param name="job_qual" value="accurate" /> 150 <param name="job_qual" value="accurate" />
148 <param name="condBackbone.use" value="false" /> 151 <param name="condBackbone.use" value="false" />
149 <param name="condSanger.use" value="true" /> 152 <param name="condSanger.use" value="true" />
151 <param name="condRoche.use" value="false" /> 154 <param name="condRoche.use" value="false" />
152 <param name="condIllumina.use" value="false" /> 155 <param name="condIllumina.use" value="false" />
153 <param name="condIonTorrent.use" value="false" /> 156 <param name="condIonTorrent.use" value="false" />
154 <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" /> 157 <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
155 </test> 158 </test>
159 -->
156 </tests> 160 </tests>
157 <help> 161 <help>
158 162
159 **What it does** 163 **What it does**
160 164
161 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.
162 166
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
163 **Citation** 173 **Citation**
164 174
165 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:
166 177
167 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 Cock, Bjoern Gruening, 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
182
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.
168 186
169 This wrapper is available to install into other Galaxy Instances via the Galaxy 187 This wrapper is available to install into other Galaxy Instances via the Galaxy
170 Tool Shed at http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler 188 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
171 189
172 </help> 190 </help>
173 </tool> 191 </tool>