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comparison bcftools_stats.xml @ 25:24e9954fec54 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
author iuc
date Tue, 02 Dec 2025 08:03:22 +0000
parents 913c052dfc71
children
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equal deleted inserted replaced
24:913c052dfc71 25:24e9954fec54
6 </macros> 6 </macros>
7 <expand macro="bio_tools" /> 7 <expand macro="bio_tools" />
8 <expand macro="requirements"> 8 <expand macro="requirements">
9 <expand macro="samtools_requirement"/> 9 <expand macro="samtools_requirement"/>
10 <expand macro="matplotlib_requirement" /> 10 <expand macro="matplotlib_requirement" />
11 <requirement type="package" version="0.12.0">tectonic</requirement> 11 <requirement type="package" version="0.15.0">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@
16 #set $input_files = [$input_file] 15 #set $input_files = [$input_file]
17 #if $inputB_file: 16 #if $inputB_file:
18 #silent $input_files.append($inputB_file) 17 #silent $input_files.append($inputB_file)
19 #end if 18 #end if
20 @PREPARE_INPUT_FILES@ 19 @PREPARE_INPUT_FILES@
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 <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" />
82 <section name="sec_restrict" expanded="false" title="Restrict to"> 81 <section name="sec_restrict" expanded="false" title="Restrict to">
83 <expand macro="macro_samples" /> 82 <expand macro="macro_samples" />
84 <expand macro="macro_apply_filters" /> 83 <expand macro="macro_apply_filters" />
85 <expand macro="macro_collapse" /> 84 <expand macro="macro_collapse" />
86 <expand macro="macro_restrict" /> 85 <expand macro="macro_region_restrict" />
87 <expand macro="macro_restrict" type="target" label_type="Target" /> 86 <expand macro="macro_target_restrict" />
88 <expand macro="macro_include" /> 87 <expand macro="macro_include" />
89 <expand macro="macro_exclude" /> 88 <expand macro="macro_exclude" />
90 </section> 89 </section>
91 <section name="sec_default" expanded="true" title="Stats options"> 90 <section name="sec_default" expanded="true" title="Stats options">
92 <param name="first_allele_only" type="boolean" truevalue="--1st-allele-only" falsevalue="" label="First allele only" 91 <param name="first_allele_only" type="boolean" truevalue="--1st-allele-only" falsevalue="" label="First allele only"
200 <!-- Test region overlap option--> 199 <!-- Test region overlap option-->
201 <test expect_num_outputs="1"> 200 <test expect_num_outputs="1">
202 <param name="input_file" ftype="vcf" value="stats.b.vcf" /> 201 <param name="input_file" ftype="vcf" value="stats.b.vcf" />
203 <param name="inputB_file" ftype="vcf" value="stats.a.vcf" /> 202 <param name="inputB_file" ftype="vcf" value="stats.a.vcf" />
204 <section name="sec_restrict"> 203 <section name="sec_restrict">
205 <param name="regions_overlap" value="1"/> 204 <conditional name="regions">
205 <param name="regions_src" value="regions" />
206 <repeat name="region_specs">
207 <param name="chrom" value="1" />
208 </repeat>
209 </conditional>
206 </section> 210 </section>
207 <output name="output_file"> 211 <output name="output_file">
208 <assert_contents> 212 <assert_contents>
209 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/> 213 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
210 <has_text_matching expression="SN\t1\tnumber of samples:\t3"/> 214 <has_text_matching expression="SN\t1\tnumber of samples:\t3"/>
233 <param name="samples" value="-" /> 237 <param name="samples" value="-" />
234 </section> 238 </section>
235 <output name="output_file"> 239 <output name="output_file">
236 <assert_contents> 240 <assert_contents>
237 <has_text_matching expression="bcftools stats --samples - "/> 241 <has_text_matching expression="bcftools stats --samples - "/>
238 <has_text_matching expression="PSC\t0\tHG00101\t0\t0\t0\t0\t0\t0\t4.8"/> 242 <has_text_matching expression="PSC\t0\tHG00101\t0\t0\t0\t0\t0\t0\t4.9"/>
239 <has_text_matching expression="PSI\t0\tHG00102\t0"/> 243 <has_text_matching expression="PSI\t0\tHG00102\t0"/>
240 </assert_contents> 244 </assert_contents>
241 </output> 245 </output>
242 </test> 246 </test>
243 </tests> 247 </tests>
258 @TARGETS_HELP@ 262 @TARGETS_HELP@
259 @EXPRESSIONS_HELP@ 263 @EXPRESSIONS_HELP@
260 264
261 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ 265 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
262 266
263 @BCFTOOLS_WIKI@ 267 @BCFTOOLS_HOWTOS@
264 ]]> 268 ]]>
265 </help> 269 </help>
266 <expand macro="citations" /> 270 <expand macro="citations" />
267 </tool> 271 </tool>