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comparison bcftools_stats.xml @ 4:5129a2b2f316 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
author iuc
date Sat, 11 Mar 2017 18:05:39 -0500
parents 92e47ae9a121
children 3afcc6474c79
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3:f8e9951c94b1 4:5129a2b2f316
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@">
3 <description>Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats</description> 3 <description>Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">stats</token> 5 <token name="@EXECUTABLE@">stats</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <expand macro="requirements" /> 8 <expand macro="requirements">
9 <requirement type="package" version="1.3.1">samtools</requirement>
10 </expand>
9 <expand macro="version_command" /> 11 <expand macro="version_command" />
10 <command detect_errors="aggressive"><![CDATA[ 12 <command detect_errors="aggressive"><![CDATA[
11 @PREPARE_ENV@ 13 @PREPARE_ENV@
12 @PREPARE_INPUT_FILES@ 14 @PREPARE_INPUT_FILES@
13 #set $section = $sec_restrict 15 #set $section = $sec_restrict
78 <param name="depth_min" type="integer" value="0" min="0" label="Depth min"/> 80 <param name="depth_min" type="integer" value="0" min="0" label="Depth min"/>
79 <param name="depth_max" type="integer" value="500" min="1" label="Depth max" /> 81 <param name="depth_max" type="integer" value="500" min="1" label="Depth max" />
80 <param name="depth_bin_size" type="integer" value="1" min="1" label="Depth bin size" /> 82 <param name="depth_bin_size" type="integer" value="1" min="1" label="Depth bin size" />
81 </when> 83 </when>
82 </conditional> 84 </conditional>
83 <param name="fasta_ref" type="data" format="data" label="Fasta Ref" optional="True" help="Reference sequence" /> 85 <expand macro="macro_fasta_ref" />
84 <expand macro="macro_exons_file" /> 86 <expand macro="macro_exons_file" />
85 <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split By Id (Ignored on multiple inputs)" 87 <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split By Id (Ignored on multiple inputs)"
86 help="Collect stats for sites with ID separately (known vs novel)" /> 88 help="Collect stats for sites with ID separately (known vs novel)" />
87 <param name="user_tstv" type="text" value="" optional="true" label="User Tstv" 89 <param name="user_tstv" type="text" value="" optional="true" label="User Tstv"
88 help="Collect Ts/Tv stats for any tag using the given binning: TAG[:min:max:binsize]" > 90 help="Collect Ts/Tv stats for any tag using the given binning: TAG[:min:max:binsize]" >