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comparison bcftools_stats.xml @ 21:b6bb8672fa3e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 96c0663be587b73bdf09ddf060cb559f28f9eba7
author iuc
date Thu, 12 Jan 2023 15:09:27 +0000
parents efc721939304
children afeffe9e655d
comparison
equal deleted inserted replaced
20:6cdba75306e8 21:b6bb8672fa3e
7 </macros> 7 </macros>
8 <expand macro="bio_tools" /> 8 <expand macro="bio_tools" />
9 <expand macro="requirements"> 9 <expand macro="requirements">
10 <expand macro="samtools_requirement"/> 10 <expand macro="samtools_requirement"/>
11 <expand macro="matplotlib_requirement" /> 11 <expand macro="matplotlib_requirement" />
12 <requirement type="package" version="0.8.0">tectonic</requirement> 12 <requirement type="package" version="0.12.0">tectonic</requirement>
13 </expand> 13 </expand>
14 <expand macro="version_command" /> 14 <expand macro="version_command" />
15 <command detect_errors="aggressive"><![CDATA[ 15 <command detect_errors="aggressive"><![CDATA[
16 @PREPARE_ENV@ 16 @PREPARE_ENV@
17 #set $input_files = [$input_file] 17 #set $input_files = [$input_file]
87 <expand macro="macro_restrict" /> 87 <expand macro="macro_restrict" />
88 <expand macro="macro_restrict" type="target" label_type="Target" /> 88 <expand macro="macro_restrict" type="target" label_type="Target" />
89 <expand macro="macro_include" /> 89 <expand macro="macro_include" />
90 <expand macro="macro_exclude" /> 90 <expand macro="macro_exclude" />
91 </section> 91 </section>
92 <section name="sec_default" expanded="true" title="Stats Options"> 92 <section name="sec_default" expanded="true" title="Stats options">
93 <param name="first_allele_only" type="boolean" truevalue="--1st-allele-only" falsevalue="" label="1St Allele Only" 93 <param name="first_allele_only" type="boolean" truevalue="--1st-allele-only" falsevalue="" label="First allele only"
94 help="Include only 1st allele at multiallelic sites" /> 94 help="Include only first allele at multiallelic sites" />
95 <conditional name="depth"> 95 <conditional name="depth">
96 <param name="set_depth" type="select" label="depth distribution: min,max,bin_size [0,500,1]"> 96 <param name="set_depth" type="select" label="Depth distribution">
97 <option value="no">use depth defaults</option> 97 <option value="no">Use depth defaults</option>
98 <option value="yes">set depth</option> 98 <option value="yes">Set depth values</option>
99 </param> 99 </param>
100 <when value="no"/> 100 <when value="no"/>
101 <when value="yes"> 101 <when value="yes">
102 <param name="depth_min" type="integer" value="0" min="0" label="Depth min"/> 102 <param name="depth_min" type="integer" value="0" min="0" label="Depth min"/>
103 <param name="depth_max" type="integer" value="500" min="1" label="Depth max" /> 103 <param name="depth_max" type="integer" value="500" min="1" label="Depth max" />
122 <when value="history"> 122 <when value="history">
123 <param name="fasta_ref" type="data" format="fasta" label="Reference genome" /> 123 <param name="fasta_ref" type="data" format="fasta" label="Reference genome" />
124 </when> 124 </when>
125 </conditional> 125 </conditional>
126 <expand macro="macro_exons_file" /> 126 <expand macro="macro_exons_file" />
127 <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split By Id (Ignored on multiple inputs)" 127 <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split by ID (ignored on multiple inputs)"
128 help="Collect stats for sites with ID separately (known vs novel)" /> 128 help="Collect stats for sites with ID separately (known vs novel)" />
129 <param name="user_tstv" type="text" value="" optional="true" label="User Tstv" 129 <param name="user_tstv" type="text" value="" optional="true" label="User Tstv"
130 help="Collect Ts/Tv stats for any tag using the given binning: TAG[:min:max:binsize]" > 130 help="Collect Ts/Tv stats for any tag using the given binning: TAG[:min:max:binsize]" >
131 <validator type="regex" message="TAG optionally followed by :min:max:binsize">^([^ \t\n\r\f\v:,](:\d+:\d+:\d+)?)?$</validator> 131 <validator type="regex" message="TAG optionally followed by :min:max:binsize">^([^ \t\n\r\f\v:,](:\d+:\d+:\d+)?)?$</validator>
132 </param> 132 </param>
133 <conditional name="afbins"> 133 <conditional name="afbins">
134 <param name="afbins_select" type="select" label="Set af-bins"> 134 <param name="afbins_select" type="select" label="Set af-bins">
135 <option value="default">use default</option> 135 <option value="default">Use default</option>
136 <option value="af_bins_list">enter bins</option> 136 <option value="af_bins_list">Enter bins</option>
137 <option value="af_bins_file">read bins from file</option> 137 <option value="af_bins_file">Read bins from file</option>
138 </param> 138 </param>
139 <when value="default"/> 139 <when value="default"/>
140 <when value="af_bins_list"> 140 <when value="af_bins_list">
141 <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)"> 141 <param name="af_bins_list" type="text" value="0.1,0.5,1" label="List of allele frequency bins" help="e.g. 0.1,0.5,1">
142 <validator type="regex" message="comma-separated list of floats of increasing value">^[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?(,[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?)*$</validator> 142 <validator type="regex" message="Comma-separated list of floats of increasing value">^[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?(,[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?)*$</validator>
143 </param> 143 </param>
144 </when> 144 </when>
145 <when value="af_bins_file"> 145 <when value="af_bins_file">
146 <param name="af_bins_file" type="data" format="tabular" label="file listing the allele frequency bins one per line"/> 146 <param name="af_bins_file" type="data" format="tabular" label="File listing the allele frequency bins one per line"/>
147 </when> 147 </when>
148 </conditional> 148 </conditional>
149 <param name="af_tag" type="text" value="" optional="true" label="allele frequency tag to use, by default estimated from AN,AC or GT"> 149 <param name="af_tag" type="text" value="" optional="true" label="Allele frequency tag to use, by default estimated from AN,AC or GT">
150 <validator type="regex" message="TAG">^\w*$</validator> 150 <validator type="regex" message="TAG">^\w*$</validator>
151 </param> 151 </param>
152 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Verbose" 152 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Verbose"
153 help="Produce verbose per-site and per-sample output" /> 153 help="Produce verbose per-site and per-sample output" />
154 </section> 154 </section>