Mercurial > repos > yhoogstrate > crossmap

comparison crossmap.xml @ 6:5ef4ac8f2956 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 7ab6217b10b7483a03140eddc9c0567551b41b62
author yhoogstrate
date Thu, 12 Nov 2015 10:42:27 -0500
parents 9da7052375b9
children 1efce8a693ca
comparison
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5:9da7052375b9 6:5ef4ac8f2956
10 <stdio> 10 <stdio>
11 <regex match="Usage: CrossMap.py" source="stdout" level="fatal"/> 11 <regex match="Usage: CrossMap.py" source="stdout" level="fatal"/>
12 <regex match=".*" source="both" level="log"/> 12 <regex match=".*" source="both" level="log"/>
13 </stdio> 13 </stdio>
14 14
15 <version_command>python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command> 15 <version_command>python $CROSSMAP_ROOT_DIR/bin/CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
16 16
17 <command><!-- First line of CrossMap has hardcoded "#!/usr/bin/python". This makes use of Galaxy's python: --> 17 <command><!-- First line of CrossMap has hardcoded "#!/usr/bin/python". This makes use of Galaxy's python: -->
18 python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py 18 python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py
19 ${multiple.input_format.replace("sam","bam")} 19 ${multiple.input_format.replace("sam","bam")}
20 20
302 </when> 302 </when>
303 </conditional> 303 </conditional>
304 </inputs> 304 </inputs>
305 305
306 <outputs> 306 <outputs>
307 <data format="text" name="output" label="${tool.name} on "> 307 <data format="text" name="output" label="${tool.name} on ${on_string}">
308 <change_format> 308 <change_format>
309 <when input="multiple.input_format" value="bam" format="bam" /> 309 <when input="multiple.input_format" value="bam" format="bam" />
310 <when input="multiple.input_format" value="sam" format="sam" /> 310 <when input="multiple.input_format" value="sam" format="sam" />
311 <when input="multiple.input_format" value="bed" format="bed" /> 311 <when input="multiple.input_format" value="bed" format="bed" />
312 <when input="multiple.input_format" value="bigwig" format="bigwig" /> 312 <when input="multiple.input_format" value="bigwig" format="bigwig" />
313 <when input="multiple.input_format" value="gff" format="gff" /> 313 <when input="multiple.input_format" value="gff" format="gff" />
314 <when input="multiple.input_format" value="vcf" format="vcf" /> 314 <when input="multiple.input_format" value="vcf" format="vcf" />
315 <when input="imultiple.nput_format" value="wig" format="bigwig" /> 315 <when input="multiple.input_format" value="wig" format="bigwig" />
316 </change_format> 316 </change_format>
317 </data> 317 </data>
318 318
319 <data format="text" name="output_unmapped" label="${tool.name} unmapped on "> 319 <data format="text" name="output_unmapped" label="${tool.name} (unmapped) on ${on_string}">
320 <filter>input_format in ["bam" , "vcf"]</filter> 320 <filter>multiple['input_format'] in ["bam" , "vcf"]</filter>
321 <change_format> 321 <change_format>
322 <when input="multiple.input_format" value="bam" format="bam" /> 322 <when input="multiple.input_format" value="bam" format="bam" />
323 <when input="multiple.input_format" value="vcf" format="vcf" /> 323 <when input="multiple.input_format" value="vcf" format="vcf" />
324 </change_format> 324 </change_format>
325 </data> 325 </data>
326 <data format="text" name="output2" label="${tool.name} on "> 326 <data format="text" name="output2" label="${tool.name} (bedgraph) on ${on_string}">
327 <filter>input_format in ["wig"]</filter> 327 <filter>multiple['input_format'] in ["wig"]</filter>
328 <change_format> 328 <change_format>
329 <when input="multiple.input_format" value="wig" format="bedgraph" /> 329 <when input="multiple.input_format" value="wig" format="bedgraph" />
330 </change_format> 330 </change_format>
331 </data> 331 </data>
332 </outputs> 332 </outputs>