Mercurial > repos > greg > gene_family_classifier
diff gene_family_classifier.xml @ 131:656614635ebf draft
Uploaded
author | greg |
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date | Thu, 06 Apr 2017 14:21:39 -0400 |
parents | fb3feee2638d |
children | 169504db8e43 |
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--- a/gene_family_classifier.xml Wed Mar 22 08:45:31 2017 -0400 +++ b/gene_family_classifier.xml Thu Apr 06 14:21:39 2017 -0400 @@ -1,16 +1,10 @@ <tool id="plant_tribes_gene_family_classifier" name="GeneFamilyClassifier" version="0.4.0"> <description>classifies gene sequences into pre-computed orthologous plant gene family clusters</description> - <requirements> - <requirement type="package" version="0.4">plant_tribes_gene_family_classifier</requirement> - </requirements> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements_gene_family_classifier" /> + <expand macro="stdio" /> <command> <![CDATA[ #if str($options_type.options_type_selector) == 'advanced': @@ -295,42 +289,8 @@ </help> <citations> - <citation type="bibtex"> - @misc{None, - journal = {None}, - author = {1. Wafula EK}, - title = {Manuscript in preparation}, - year = {None}, - url = {https://github.com/dePamphilis/PlantTribes},} - </citation> - <citation type="bibtex"> - @article{Sasidharan2012, - journal = {Nucleic Acids Research}, - author = {2. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A}, - title = {GFam: a platform for automatic annotation of gene families}, - year = {2012}, - pages = {gks631},} - </citation> - <citation type="bibtex"> - @article{Li2003, - journal = {Genome Research} - author = {3. Li L, Stoeckert CJ, Roos DS}, - title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes}, - year = {2003}, - volume = {13}, - number = {9}, - pages = {2178-2189},} - </citation> - <citation type="bibtex"> - @article{Emms2015, - journal = {Genome Biology} - author = {4. Emms DM, Kelly S}, - title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy}, - year = {2015}, - volume = {16}, - number = {1}, - pages = {157},} - </citation> + <expand macro="citation1" /> + <expand macro="citations2to4" /> <citation type="bibtex"> @article{Altschul1990, journal = {Journal of molecular biology}