Mercurial > repos > iuc > bcftools_call
comparison bcftools_call.xml @ 3:5337db17a5f7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 44bebb8a97d64015cbba59f0663e2541035112b6
author | iuc |
---|---|
date | Mon, 03 Oct 2016 12:19:38 -0400 |
parents | 8959eda17fca |
children | 6d2a5f0859cf |
comparison
equal
deleted
inserted
replaced
2:99dff9c8b2f3 | 3:5337db17a5f7 |
---|---|
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)<FLOAT with -c" /> | 137 <param name="pval_threshold" type="float" label="Pval Threshold" value="0.5" optional="True" help="variant if P(ref|D)<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> |