Mercurial > repos > iuc > bcftools_roh

comparison bcftools_roh.xml @ 2:942f744b02db draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 5725fea947162618d77de7b8011d18b2f16c7094
author iuc
date Sat, 21 Jan 2017 06:57:12 -0500
parents cf23cddde150
children 81049a32c117
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1:cc6371864d34 2:942f744b02db
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.1">
3 <description>HMM model for detecting runs of autozygosity</description> 3 <description>HMM model for detecting runs of autozygosity</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">roh</token> 5 <token name="@EXECUTABLE@">roh</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
77 <param name="skip_indels" type="boolean" truevalue="--skip-indels" falsevalue="" label="Skip Indels" help="Skip indels as their genotypes are enriched for errors" /> 77 <param name="skip_indels" type="boolean" truevalue="--skip-indels" falsevalue="" label="Skip Indels" help="Skip indels as their genotypes are enriched for errors" />
78 <param name="genetic_map" type="data" format="data" label="Genetic Map" optional="True" help="Genetic map in IMPUTE2 format, single file or mask, where string &quot;{CHROM}&quot; is replaced with chromosome name" /> 78 <param name="genetic_map" type="data" format="data" label="Genetic Map" optional="True" help="Genetic map in IMPUTE2 format, single file or mask, where string &quot;{CHROM}&quot; is replaced with chromosome name" />
79 <param name="rec_rate" type="float" label="Rec Rate" optional="True" help="Constant recombination rate per bp" /> 79 <param name="rec_rate" type="float" label="Rec Rate" optional="True" help="Constant recombination rate per bp" />
80 </section> 80 </section>
81 <section name="sec_hmm" expanded="true" title="HMM Options"> 81 <section name="sec_hmm" expanded="true" title="HMM Options">
82 <param name="hw_to_az" type="float" label="Hw To Az" default="6.7e-8" optional="True" help="P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state" /> 82 <param name="hw_to_az" type="float" label="Hw To Az" value="6.7e-8" optional="True" help="P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state" />
83 <param name="az_to_hw" type="float" label="Az To Hw" default="5e-9" optional="True" help="P(HW|AZ) transition probability from AZ to HW state" /> 83 <param name="az_to_hw" type="float" label="Az To Hw" value="5e-9" optional="True" help="P(HW|AZ) transition probability from AZ to HW state" />
84 <param name="viterbi_training" type="boolean" truevalue="--viterbi-training" falsevalue="" label="Viterbi Training" help="Perform Viterbi training to estimate transition probabilities" /> 84 <param name="viterbi_training" type="boolean" truevalue="--viterbi-training" falsevalue="" label="Viterbi Training" help="Perform Viterbi training to estimate transition probabilities" />
85 </section> 85 </section>
86 </inputs> 86 </inputs>
87 <outputs> 87 <outputs>
88 <data name="output_file" format="tabular"/> 88 <data name="output_file" format="tabular"/>