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comparison gene_family_classifier.xml @ 131:656614635ebf draft

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author greg
date Thu, 06 Apr 2017 14:21:39 -0400
parents fb3feee2638d
children 169504db8e43
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130:fb3feee2638d 131:656614635ebf
1 <tool id="plant_tribes_gene_family_classifier" name="GeneFamilyClassifier" version="0.4.0"> 1 <tool id="plant_tribes_gene_family_classifier" name="GeneFamilyClassifier" version="0.4.0">
2 <description>classifies gene sequences into pre-computed orthologous plant gene family clusters</description> 2 <description>classifies gene sequences into pre-computed orthologous plant gene family clusters</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.4">plant_tribes_gene_family_classifier</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <stdio> 6 <expand macro="requirements_gene_family_classifier" />
7 <!-- Anything other than zero is an error --> 7 <expand macro="stdio" />
8 <exit_code range="1:" />
9 <exit_code range=":-1" />
10 <!-- In case the return code has not been set propery check stderr too -->
11 <regex match="Error:" />
12 <regex match="Exception:" />
13 </stdio>
14 <command> 8 <command>
15 <![CDATA[ 9 <![CDATA[
16 #if str($options_type.options_type_selector) == 'advanced': 10 #if str($options_type.options_type_selector) == 'advanced':
17 #set specify_super_orthogroups_cond = $options_type.specify_super_orthogroups_cond 11 #set specify_super_orthogroups_cond = $options_type.specify_super_orthogroups_cond
18 #set specify_super_orthogroups = $specify_super_orthogroups_cond.specify_super_orthogroups 12 #set specify_super_orthogroups = $specify_super_orthogroups_cond.specify_super_orthogroups
293 287
294 * **Coding sequences fasta file** - select coding sequences fasta file corresponding to the proteins fasta file from your history. 288 * **Coding sequences fasta file** - select coding sequences fasta file corresponding to the proteins fasta file from your history.
295 289
296 </help> 290 </help>
297 <citations> 291 <citations>
298 <citation type="bibtex"> 292 <expand macro="citation1" />
299 @misc{None, 293 <expand macro="citations2to4" />
300 journal = {None},
301 author = {1. Wafula EK},
302 title = {Manuscript in preparation},
303 year = {None},
304 url = {https://github.com/dePamphilis/PlantTribes},}
305 </citation>
306 <citation type="bibtex">
307 @article{Sasidharan2012,
308 journal = {Nucleic Acids Research},
309 author = {2. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A},
310 title = {GFam: a platform for automatic annotation of gene families},
311 year = {2012},
312 pages = {gks631},}
313 </citation>
314 <citation type="bibtex">
315 @article{Li2003,
316 journal = {Genome Research}
317 author = {3. Li L, Stoeckert CJ, Roos DS},
318 title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes},
319 year = {2003},
320 volume = {13},
321 number = {9},
322 pages = {2178-2189},}
323 </citation>
324 <citation type="bibtex">
325 @article{Emms2015,
326 journal = {Genome Biology}
327 author = {4. Emms DM, Kelly S},
328 title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
329 year = {2015},
330 volume = {16},
331 number = {1},
332 pages = {157},}
333 </citation>
334 <citation type="bibtex"> 294 <citation type="bibtex">
335 @article{Altschul1990, 295 @article{Altschul1990,
336 journal = {Journal of molecular biology} 296 journal = {Journal of molecular biology}
337 author = {5. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ}, 297 author = {5. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ},
338 title = {Basic local alignment search tool}, 298 title = {Basic local alignment search tool},