Mercurial > repos > veg > mmvc
view mmvc.xml @ 0:a3f7993dca52 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit d4006c1381bdece9d754bdfebb80efb61040d6e9-dirty
author | veg |
---|---|
date | Wed, 18 Apr 2018 16:28:28 -0400 |
parents | |
children |
line wrap: on
line source
<?xml version="1.0"?> <tool id="mmvc" version="1.0.2" name="mmvc"> <description>Multinomial mixture variant caller</description> <requirements> <requirement type="package" version="1.0.2">mmvc</requirement> </requirements> <stdio> <exit_code range="1:"/> </stdio> <version_command/> <command><![CDATA[ mmvc -j '$json_report' -f '$filter_msa' #if str($options.advanced) == 'advanced': -g $options.grid_density -c $options.chain_length -b $options.burnin_fraction -t $options.target_rate -p $options.posterior_threshold #end if '$input_fasta' ]]></command> <inputs> <param name="input_fasta" label="Input FASTA" type="data" format="fasta"/> <conditional name="options"> <param label="Additional options" name="advanced" type="select"> <option value="defaults">Use defaults</option> <option value="advanced">Specify additional parameters</option> </param> <when value="defaults"/> <when value="advanced"> <param label="GRID_DENSITY" name="grid_density" type="integer" value="10"/> <param label="CHAIN_LENGTH" name="chain_length" type="integer" value="2000000"/> <param label="BURNIN_FRACTION" name="burnin_fraction" type="float" value="0.5"/> <param label="TARGET_RATE" name="target_rate" type="float" value="0.01"/> <param label="POSTERIOR_THRESHOLD" name="posterior_threshold" type="float" value="0.95"/> </when> </conditional> </inputs> <outputs> <data format="json" name="json_report"/> <data format="fasta" name="filter_msa"/> </outputs> <tests> <test> <param name="input_fasta" value="mmvc-in1.fa"/> <param name="advanced" value="advanced"/> <param name="chain_length" value="200"/> <output name="json_report"> <assert_contents> <has_text text="variant"/> <has_text text="weight"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ MMVC ---- Multinomial mixture variant caller ]]></help> <citations> <citation type="bibtex"> @UNPUBLISHED{spond, author = "Sergei Kosakovsky Pond", title = "HyPhy: Hypothesis Testing using Phylogenies", year = "2000", note = "http://hyphy.org/", url = "http://hyphy.org/"} </citation> </citations> </tool>