Mercurial > repos > iuc > bcftools_stats

comparison bcftools_stats.xml @ 18:efc721939304 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author iuc
date Tue, 20 Sep 2022 12:15:34 +0000
parents 28f9bae3ffd1
children b6bb8672fa3e
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equal deleted inserted replaced
17:b5bc75952824 18:efc721939304
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@+galaxy1" profile="18.01"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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>
196 <has_text_matching expression="ST\t0\tA>C\t16"/> 196 <has_text_matching expression="ST\t0\tA>C\t16"/>
197 </assert_contents> 197 </assert_contents>
198 </output> 198 </output>
199 <output name="output_pdf" file="summary.pdf" compare="sim_size" delta="25000" /> 199 <output name="output_pdf" file="summary.pdf" compare="sim_size" delta="25000" />
200 </test> 200 </test>
201 <!-- Test region overlap option-->
202 <test>
203 <param name="input_file" ftype="vcf" value="stats.b.vcf" />
204 <param name="inputB_file" ftype="vcf" value="stats.a.vcf" />
205 <section name="sec_restrict">
206 <param name="regions_overlap" value="1"/>
207 </section>
208 <output name="output_file">
209 <assert_contents>
210 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
211 <has_text_matching expression="SN\t1\tnumber of samples:\t3"/>
212 </assert_contents>
213 </output>
214 <assert_command>
215 <has_text text="--regions-overlap" />
216 </assert_command>
217 </test>
218 <!-- Test VCF.gz input file -> REQUIRES https://github.com/galaxyproject/galaxy/pull/14605
219 <test>
220 <param name="input_file" value="mpileup.vcf.gz" />
221 <output name="output_file">
222 <assert_contents>
223 <has_text_matching expression="bcftools stats input0.vcf.gz"/>
224 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
225 <has_text_matching expression="SN\t0\tnumber of records:\t4103"/>
226 </assert_contents>
227 </output>
228 </test>
229 -->
230 <!-- Test modification in samples option -->
231 <test>
232 <param name="input_file" ftype="vcf" value="mpileup.vcf" />
233 <section name="sec_restrict">
234 <param name="samples" value="-" />
235 </section>
236 <output name="output_file">
237 <assert_contents>
238 <has_text_matching expression="bcftools stats --samples - "/>
239 <has_text_matching expression="PSC\t0\tHG00101\t0\t0\t0\t0\t0\t0\t4.8"/>
240 <has_text_matching expression="PSI\t0\tHG00102\t0"/>
241 </assert_contents>
242 </output>
243 </test>
201 </tests> 244 </tests>
202 <help><![CDATA[ 245 <help><![CDATA[
203 ===================================== 246 =====================================
204 bcftools @EXECUTABLE@ 247 bcftools @EXECUTABLE@
205 ===================================== 248 =====================================