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comparison blat_wrapper.xml @ 1:c4ad58c4bc7d draft

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Add version_command element. Add test case from Joachim Jacob's blat wrapper: http://testtoolshed.g2.bx.psu.edu/view/joachim-jacob/blat . Add readme section to tool_dependencies.xml .
author crs4
date Mon, 28 Oct 2013 12:40:29 -0400
parents 0a71a7d35d09
children 6265acc179ff
comparison
equal deleted inserted replaced
0:0a71a7d35d09 1:c4ad58c4bc7d
1 <tool id="blat_wrapper" name="BLAT" version="0.2"> 1 <tool id="blat_wrapper" name="BLAT" version="0.2">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="35">blat</requirement> 4 <requirement type="package" version="35">blat</requirement>
5 </requirements> 5 </requirements>
6 <version_command>blat|head -n 1</version_command>
6 <command> 7 <command>
7 blat $database $query -t=$databaseType.databaseType_select -q=$databaseType.queryType 8 blat $database $query -t=$databaseType.databaseType_select -q=$databaseType.queryType
8 #if str($databaseType.tileSize) 9 #if str($databaseType.tileSize)
9 -tileSize=$databaseType.tileSize 10 -tileSize=$databaseType.tileSize
10 #end if 11 #end if
193 <when input="out" value="maf" format="maf" /> 194 <when input="out" value="maf" format="maf" />
194 <when input="out" value="blast8" format="tabular" /> 195 <when input="out" value="blast8" format="tabular" />
195 </change_format> 196 </change_format>
196 </data> 197 </data>
197 </outputs> 198 </outputs>
198
199 <tests> 199 <tests>
200 <test>
201 <param name="database" value="databasetest1.fasta" ftype="fasta" />
202 <param name="query" value="input83.fasta" ftype="fasta" />
203 <param name="databaseType_select" value="dna" />
204 <param name="queryType" value="dna" />
205 <param name="tileSize" value="11" />
206 <param name="minMatch" value="2" />
207 <param name="stepSize" value="11" />
208 <param name="oneOff" value="false" />
209 <param name="minScore" value="30" />
210 <param name="maxGap" value="2" />
211 <param name="mask_select" value="lower" />
212 <param name="qMask" value="lower" />
213 <param name="trimT" value="true" />
214 <param name="noTrimA" value="false" />
215 <param name="fine" value="false" />
216 <param name="maxIntron" value="750000" />
217 <param name="extendThroughN" value="false" />
218 <param name="out" value="blast8" />
219 <output name="logfile" file="log.txt" />
220 <output name="output" file="outputtest1.txt" />
221 </test>
200 </tests> 222 </tests>
201 <help> 223 <help>
202 **What it does** 224 **What it does**
203 225
204 BLAT produces two major classes of alignments: 226 BLAT produces two major classes of alignments: