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comparison bcftools_stats.xml @ 5:64db9662b6b3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
author iuc
date Thu, 13 Apr 2017 16:23:58 -0400
parents e37d2899945c
children 96fe8635d07d
comparison
equal deleted inserted replaced
4:e37d2899945c 5:64db9662b6b3
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> 9 <expand macro="samtools_requirement"/>
10 <requirement type="package" version="2.0.0">matplotlib</requirement>
10 </expand> 11 </expand>
11 <expand macro="version_command" /> 12 <expand macro="version_command" />
12 <command detect_errors="aggressive"><![CDATA[ 13 <command detect_errors="aggressive"><![CDATA[
13 @PREPARE_ENV@ 14 @PREPARE_ENV@
14 @PREPARE_INPUT_FILES@ 15 @PREPARE_INPUT_FILES@
15 #set $section = $sec_restrict 16 #set $section = $sec_restrict
16 @PREPARE_TARGETS_FILE@ 17 @PREPARE_TARGETS_FILE@
18 @PREPARE_REGIONS_FILE@
17 ## Stats section 19 ## Stats section
18 #set $section = $sec_default 20 #set $section = $sec_default
19 @PREPARE_FASTA_REF@ 21 @PREPARE_FASTA_REF@
20 @PREPARE_EXONS_FILE@ 22 @PREPARE_EXONS_FILE@
21 23
29 #if $section.depth.set_depth == 'yes': 31 #if $section.depth.set_depth == 'yes':
30 --depth "${section.depth.depth_min},${section.depth.depth_max},${section.depth.depth_bin_size}" 32 --depth "${section.depth.depth_min},${section.depth.depth_max},${section.depth.depth_bin_size}"
31 #end if 33 #end if
32 #if $section.user_tstv: 34 #if $section.user_tstv:
33 --user-tstv "${section.user_tstv}" 35 --user-tstv "${section.user_tstv}"
36 #end if
37 #if $section.afbins.afbins_select == 'af_bins_list':
38 --af-bins $section.afbins.af_bins_list
39 #elif $section.afbins.afbins_select == 'af_bins_file':
40 --af-bins $section.afbins.af_bins_file
41 #end if
42 #if $section.af_tag:
43 --af-tag "${section.af_tag}"
34 #end if 44 #end if
35 #if len($input_vcfs) == 1: 45 #if len($input_vcfs) == 1:
36 ${section.split_by_ID} 46 ${section.split_by_ID}
37 #end if 47 #end if
38 ${section.verbose} 48 ${section.verbose}
87 <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split By Id (Ignored on multiple inputs)" 97 <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split By Id (Ignored on multiple inputs)"
88 help="Collect stats for sites with ID separately (known vs novel)" /> 98 help="Collect stats for sites with ID separately (known vs novel)" />
89 <param name="user_tstv" type="text" value="" optional="true" label="User Tstv" 99 <param name="user_tstv" type="text" value="" optional="true" label="User Tstv"
90 help="Collect Ts/Tv stats for any tag using the given binning: TAG[:min:max:binsize]" > 100 help="Collect Ts/Tv stats for any tag using the given binning: TAG[:min:max:binsize]" >
91 <validator type="regex" message="TAG optionally followed by :min:max:binsize">^([^ \t\n\r\f\v:,](:\d+:\d+:\d+)?)?$</validator> 101 <validator type="regex" message="TAG optionally followed by :min:max:binsize">^([^ \t\n\r\f\v:,](:\d+:\d+:\d+)?)?$</validator>
92 102 </param>
103 <conditional name="afbins">
104 <param name="afbins_select" type="select" label="Set af-bins">
105 <option value="default">use default</option>
106 <option value="af_bins_list">enter bins</option>
107 <option value="af_bins_file">read bins from file</option>
108 </param>
109 <when value="default"/>
110 <when value="af_bins_list">
111 <param name="af_bins_list" type="text" value="0.1,0.5,1" label="list of allele frequency bins (e.g. 0.1,0.5,1)">
112 <validator type="regex" message="comma-separated list of floats of increasing value">^[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?(,[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?)*$</validator>
113 </param>
114 </when>
115 <when value="af_bins_file">
116 <param name="af_bins_file" type="data" format="tabular" label="file listing the allele frequency bins one per line"/>
117 </when>
118 </conditional>
119 <param name="af_tag" type="text" value="" optional="true" label="allele frequency tag to use, by default estimated from AN,AC or GT">
120 <validator type="regex" message="TAG">^\w*$</validator>
93 </param> 121 </param>
94 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Verbose" 122 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Verbose"
95 help="Produce verbose per-site and per-sample output" /> 123 help="Produce verbose per-site and per-sample output" />
96 </section> 124 </section>
97 <param name="plot_title" type="text" value="" optional="true" label="Create a plots pdf with this title"> 125 <param name="plot_title" type="text" value="" optional="true" label="Create a plots pdf with this title">