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comparison bcftools_stats.xml @ 8:e3c64225cbe6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
author iuc
date Wed, 05 Jun 2019 13:00:32 -0400
parents baa8823f8073
children ef2cc5ac23bc
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7:baa8823f8073 8:e3c64225cbe6
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="@TOOL_VERSION@"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">
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 <expand macro="samtools_requirement"/> 9 <expand macro="samtools_requirement"/>
10 <requirement type="package" version="3.0.2">matplotlib</requirement> 10 <expand macro="matplotlib_requirement" />
11 <requirement type="package" version="0.1.11">tectonic</requirement> 11 <requirement type="package" version="0.1.11">tectonic</requirement>
12 </expand> 12 </expand>
13 <expand macro="version_command" /> 13 <expand macro="version_command" />
14 <command detect_errors="aggressive"><![CDATA[ 14 <command detect_errors="aggressive"><![CDATA[
15 @PREPARE_ENV@ 15 @PREPARE_ENV@
20 @PREPARE_INPUT_FILES@ 20 @PREPARE_INPUT_FILES@
21 #set $section = $sec_restrict 21 #set $section = $sec_restrict
22 @PREPARE_TARGETS_FILE@ 22 @PREPARE_TARGETS_FILE@
23 @PREPARE_REGIONS_FILE@ 23 @PREPARE_REGIONS_FILE@
24 ## Stats section 24 ## Stats section
25 #set $section = $sec_default.reference_source
26 @PREPARE_FASTA_REF@
25 #set $section = $sec_default 27 #set $section = $sec_default
26 @PREPARE_FASTA_REF@
27 @PREPARE_EXONS_FILE@ 28 @PREPARE_EXONS_FILE@
28 29
29 bcftools @EXECUTABLE@ 30 bcftools @EXECUTABLE@
30 31
31 ## Stats section 32 ## Stats section
33 #set $section = $sec_default.reference_source
34 @FASTA_REF@
32 #set $section = $sec_default 35 #set $section = $sec_default
33 @FASTA_REF@
34 @EXONS_FILE@ 36 @EXONS_FILE@
35 ${section.first_allele_only} 37 ${section.first_allele_only}
36 #if $section.depth.set_depth == 'yes': 38 #if $section.depth.set_depth == 'yes':
37 --depth ${section.depth.depth_min},${section.depth.depth_max},${section.depth.depth_bin_size} 39 --depth ${section.depth.depth_min},${section.depth.depth_max},${section.depth.depth_bin_size}
38 #end if 40 #end if
79 <param name="inputB_file" type="data" format="vcf,vcf_bgzip,bcf" optional="true" label="Optional VCF/BCF Data to compare against" help="When this second dataset is also specified, separate stats for intersection and the complements are generated" /> 81 <param name="inputB_file" type="data" format="vcf,vcf_bgzip,bcf" optional="true" label="Optional VCF/BCF Data to compare against" help="When this second dataset is also specified, separate stats for intersection and the complements are generated" />
80 <section name="sec_restrict" expanded="false" title="Restrict to"> 82 <section name="sec_restrict" expanded="false" title="Restrict to">
81 <expand macro="macro_samples" /> 83 <expand macro="macro_samples" />
82 <expand macro="macro_apply_filters" /> 84 <expand macro="macro_apply_filters" />
83 <expand macro="macro_collapse" /> 85 <expand macro="macro_collapse" />
84 <expand macro="macro_regions" /> 86 <expand macro="macro_restrict" />
85 <expand macro="macro_targets" /> 87 <expand macro="macro_restrict" type="target" label_type="Target" />
86 <expand macro="macro_include" /> 88 <expand macro="macro_include" />
87 <expand macro="macro_exclude" /> 89 <expand macro="macro_exclude" />
88 </section> 90 </section>
89 <section name="sec_default" expanded="true" title="Stats Options"> 91 <section name="sec_default" expanded="true" title="Stats Options">
90 <param name="first_allele_only" type="boolean" truevalue="--1st-allele-only" falsevalue="" label="1St Allele Only" 92 <param name="first_allele_only" type="boolean" truevalue="--1st-allele-only" falsevalue="" label="1St Allele Only"
99 <param name="depth_min" type="integer" value="0" min="0" label="Depth min"/> 101 <param name="depth_min" type="integer" value="0" min="0" label="Depth min"/>
100 <param name="depth_max" type="integer" value="500" min="1" label="Depth max" /> 102 <param name="depth_max" type="integer" value="500" min="1" label="Depth max" />
101 <param name="depth_bin_size" type="integer" value="1" min="1" label="Depth bin size" /> 103 <param name="depth_bin_size" type="integer" value="1" min="1" label="Depth bin size" />
102 </when> 104 </when>
103 </conditional> 105 </conditional>
104 <expand macro="macro_fasta_ref" /> 106 <conditional name="reference_source">
107 <param name="reference_source_selector" type="select" label="Choose a reference genome">
108 <option value="">Run without a reference genome</option>
109 <option value="cached">Use a built-in genome</option>
110 <option value="history">Use a genome from the history</option>
111 </param>
112 <when value="" />
113 <when value="cached">
114 <param name="fasta_ref" type="select" label="Reference genome">
115 <options from_data_table="fasta_indexes">
116 <filter type="data_meta" column="1" key="dbkey" ref="input_file" />
117 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
118 </options>
119 </param>
120 </when>
121 <when value="history">
122 <param name="fasta_ref" type="data" format="fasta" label="Reference genome" />
123 </when>
124 </conditional>
105 <expand macro="macro_exons_file" /> 125 <expand macro="macro_exons_file" />
106 <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split By Id (Ignored on multiple inputs)" 126 <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split By Id (Ignored on multiple inputs)"
107 help="Collect stats for sites with ID separately (known vs novel)" /> 127 help="Collect stats for sites with ID separately (known vs novel)" />
108 <param name="user_tstv" type="text" value="" optional="true" label="User Tstv" 128 <param name="user_tstv" type="text" value="" optional="true" label="User Tstv"
109 help="Collect Ts/Tv stats for any tag using the given binning: TAG[:min:max:binsize]" > 129 help="Collect Ts/Tv stats for any tag using the given binning: TAG[:min:max:binsize]" >
152 </assert_contents> 172 </assert_contents>
153 </output> 173 </output>
154 </test> 174 </test>
155 <test> 175 <test>
156 <param name="input_file" ftype="vcf" value="mpileup.vcf" /> 176 <param name="input_file" ftype="vcf" value="mpileup.vcf" />
177 <section name="sec_default">
178 <expand macro="test_using_reference" select_from="cached" ref="mpileup" />
179 </section>
180 <output name="output_file">
181 <assert_contents>
182 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
183 <has_text_matching expression="SN\t0\tnumber of records:\t4103"/>
184 <has_text_matching expression="ST\t0\tA>C\t16"/>
185 </assert_contents>
186 </output>
187 </test>
188 <test>
189 <param name="input_file" ftype="vcf" value="mpileup.vcf" />
157 <param name="plot_title" value="Plot for mpileup.vcf" /> 190 <param name="plot_title" value="Plot for mpileup.vcf" />
158 <output name="output_file"> 191 <output name="output_file">
159 <assert_contents> 192 <assert_contents>
160 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/> 193 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
161 <has_text_matching expression="SN\t0\tnumber of records:\t4103"/> 194 <has_text_matching expression="SN\t0\tnumber of records:\t4103"/>