Mercurial > repos > iuc > bcftools_stats
comparison bcftools_stats.xml @ 8:e3c64225cbe6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
author | iuc |
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date | Wed, 05 Jun 2019 13:00:32 -0400 |
parents | baa8823f8073 |
children | ef2cc5ac23bc |
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7:baa8823f8073 | 8:e3c64225cbe6 |
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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"/> |