Mercurial > repos > dereeper > snmf
diff snmf.xml @ 6:0ba60156e25f draft
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
| author | dereeper |
|---|---|
| date | Mon, 16 Apr 2018 08:57:17 -0400 |
| parents | 84becfc8c803 |
| children | 22aee300afdf |
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--- a/snmf.xml Fri Feb 09 01:30:26 2018 -0500 +++ b/snmf.xml Mon Apr 16 08:57:17 2018 -0400 @@ -1,5 +1,5 @@ -<tool id="snmf" name="sNMF" version="1.2"> - <description>a population structure from large SNP genotype datasets</description> +<tool id="snmf" name="sNMF" version="2.0.0"> + <description>Fast and efficient program for estimating individual ancestry coefficients</description> <requirements> <requirement type="binary">perl</requirement> <requirement type="package" version="1.6.924">perl-bioperl</requirement> @@ -28,22 +28,22 @@ <tests> <test> - <param name="vcf" value="input.vcf" /> + <param name="vcf" value="snmf_input.vcf" /> <param name="kmin" value="2" /> <param name="kmax" value="5" /> <param name="threshold_group" value="50" /> - <output name="best_k_output" file="output" compare="sim_size" > + <output name="best_k_output" file="snmf_output" compare="sim_size" > <assert_contents> <has_n_columns n="4" /> <has_line_matching expression=".*\s\d\..*" /> </assert_contents> </output> - <output name="best_k_groups" file="groups" compare="sim_size" > + <output name="best_k_groups" file="snmf_groups" compare="sim_size" > <assert_contents> <has_line_matching expression=".*;.*" /> </assert_contents> </output> - <output name="outputs" file="outputs.Q" compare="sim_size" > + <output name="outputs" file="snmf_outputs.Q" compare="sim_size" > <assert_contents> <has_line_matching expression=".*\s\d\..*" /> </assert_contents> @@ -52,33 +52,52 @@ </test> </tests> - <help> - + <help><![CDATA[ .. class:: infomark -**Program encapsulated in Galaxy by Southgreen** +**sNMF** version 1.2 + +.. class:: infomark + +**Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA) .. class:: infomark -**sNMF version 1.2** +**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr ------ +--------------------------------------------------- -=========== - Overview: -=========== +==== +sNMF +==== -Fast and efficient program for estimating individual admixture coefficients based on sparse non-negative matrix factorization and population genetics. +----------- +Description +----------- ------ - -For further informations, please visite the sNMF_ website. + | Fast and efficient program for estimating individual admixture coefficients based on sparse non-negative matrix factorization and population genetics. + | For further informations, please visit the sNMF website_. -.. _sNMF: http://membres-timc.imag.fr/Olivier.Francois/snmf/index.htm - </help> +.. _website: http://membres-timc.imag.fr/Olivier.Francois/snmf/index.htm + +------------ +Dependencies +------------ +sNMF + snmf_ 1.2, Conda version +PLINK + plink_ 1.90b4, Conda version +Bioperl + perl-bioperl_ 1.6.924, Conda version + +.. _snmf: https://anaconda.org/bioconda/snmf +.. _plink: https://anaconda.org/bioconda/plink +.. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl + + ]]></help> <citations> -<citation type="doi" >10.1534/genetics.113.160572</citation> + <citation type="doi">10.1534/genetics.113.160572</citation> </citations> </tool>