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comparison bcftools_call.xml @ 4:a4f3b1dbb345 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 06:51:16 -0500
parents 0812cba3c4c8
children 3e85f6c5cf8e
comparison
equal deleted inserted replaced
3:ab7fa65eedbe 4:a4f3b1dbb345
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>SNP/indel variant calling from VCF/BCF</description> 3 <description>SNP/indel variant calling from VCF/BCF</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">call</token> 5 <token name="@EXECUTABLE@">call</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
112 <expand macro="macro_targets_file"/> 112 <expand macro="macro_targets_file"/>
113 <param name="insert_missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert Missed" help="output also sites missed by mpileup but present in -T" /> 113 <param name="insert_missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert Missed" help="output also sites missed by mpileup but present in -T" />
114 </when> 114 </when>
115 <when value="trio"> 115 <when value="trio">
116 <expand macro="macro_targets" /> 116 <expand macro="macro_targets" />
117 <param name="novel_rate" type="float" label="Novel Rate" default="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" /> 117 <param name="novel_rate" type="float" label="Novel Rate" value="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" />
118 </when> 118 </when>
119 </conditional> 119 </conditional>
120 <param name="gvcf" type="integer" label="gvcf" optional="True" help="group non-variant sites into gVCF blocks by minimum per-sample DP" /> 120 <param name="gvcf" type="integer" label="gvcf" optional="True" help="group non-variant sites into gVCF blocks by minimum per-sample DP" />
121 </when> 121 </when>
122 <when value="consensus"> 122 <when value="consensus">
126 <option value="trio">trio - call genotypes given the father-mother-child constraint</option> 126 <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
127 </param> 127 </param>
128 <when value="none"> 128 <when value="none">
129 </when> 129 </when>
130 <when value="trio"> 130 <when value="trio">
131 <param name="novel_rate" type="float" label="Novel Rate" default="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" /> 131 <param name="novel_rate" type="float" label="Novel Rate" value="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" />
132 </when> 132 </when>
133 </conditional> 133 </conditional>
134 <expand macro="macro_targets" /> 134 <expand macro="macro_targets" />
135 </when> 135 </when>
136 </conditional> 136 </conditional>
137 <param name="pval_threshold" type="float" label="Pval Threshold" default="0.5" optional="True" help="variant if P(ref|D)&lt;FLOAT with -c" /> 137 <param name="pval_threshold" type="float" label="Pval Threshold" value="0.5" optional="True" help="variant if P(ref|D)&lt;FLOAT with -c" />
138 <param name="prior" type="float" label="Prior" default="1.1e-3" optional="True" help="mutation rate (use bigger for greater sensitivity)" /> 138 <param name="prior" type="float" label="Prior" value="1.1e-3" optional="True" help="mutation rate (use bigger for greater sensitivity)" />
139 </section> 139 </section>
140 <section name="sec_file_format" expanded="false" title="File format Options"> 140 <section name="sec_file_format" expanded="false" title="File format Options">
141 <param name="ploidy" type="select" label="Select Predefined Ploidy" optional="true"> 141 <param name="ploidy" type="select" label="Select Predefined Ploidy" optional="true">
142 <option value="GRCh37">GRCh37 - Human Genome reference assembly GRCh37 / hg19</option> 142 <option value="GRCh37">GRCh37 - Human Genome reference assembly GRCh37 / hg19</option>
143 <option value="GRCh38">GRCh37 - Human Genome reference assembly GRCh38 / hg38</option> 143 <option value="GRCh38">GRCh37 - Human Genome reference assembly GRCh38 / hg38</option>