Mercurial > repos > dereeper > snmf
view snmf.xml @ 5:84becfc8c803 draft
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author | dereeper |
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date | Fri, 09 Feb 2018 01:30:26 -0500 |
parents | 9a1729b89405 |
children | 0ba60156e25f |
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<tool id="snmf" name="sNMF" version="1.2"> <description>a population structure from large SNP genotype datasets</description> <requirements> <requirement type="binary">perl</requirement> <requirement type="package" version="1.6.924">perl-bioperl</requirement> <requirement type="package" version="1.2">snmf</requirement> <requirement type="package" version="1.90">plink</requirement> </requirements> <stdio> <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> <exit_code range="1:" level="fatal" /> </stdio> <command interpreter="bash">./snmf.sh $vcf $outputs $logs $best_k_output $best_k_logfile $kmin $kmax $best_k_groups $threshold_group </command> <inputs> <param format="vcf" name="vcf" type="data" label="VCF file" help="VCF file"/> <param type="text" name="kmin" label="K min" value="2"/> <param type="text" name="kmax" label="K max" value="5"/> <param type="text" name="threshold_group" label="Minimum admixture proportion percentage for group assignation" value="50"/> </inputs> <outputs> <data format="txt" name="best_k_output" label="Best K Output"/> <data format="txt" name="best_k_groups" label="Best K Groups"/> <data format="txt" name="best_k_logfile" label="Best K Logfile"/> <data format="txt" name="outputs" label="All Outputs"/> <data format="txt" name="logs" label="All Logs"/> </outputs> <tests> <test> <param name="vcf" value="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" > <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" > <assert_contents> <has_line_matching expression=".*;.*" /> </assert_contents> </output> <output name="outputs" file="outputs.Q" compare="sim_size" > <assert_contents> <has_line_matching expression=".*\s\d\..*" /> </assert_contents> </output> </test> </tests> <help> .. class:: infomark **Program encapsulated in Galaxy by Southgreen** .. class:: infomark **sNMF version 1.2** ----- =========== Overview: =========== Fast and efficient program for estimating individual admixture coefficients based on sparse non-negative matrix factorization and population genetics. ----- For further informations, please visite the sNMF_ website. .. _sNMF: http://membres-timc.imag.fr/Olivier.Francois/snmf/index.htm </help> <citations> <citation type="doi" >10.1534/genetics.113.160572</citation> </citations> </tool>