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comparison lofreq_call.xml @ 7:4805fe3d8fda draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2
author iuc
date Wed, 06 Jul 2022 09:25:57 +0000
parents e1461b5c52a0
children b11e8e9c23bf
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6:e1461b5c52a0 7:4805fe3d8fda
1 <tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy1" profile="18.01"> 1 <tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy2" profile="18.01">
2 <description>with LoFreq</description> 2 <description>with LoFreq</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
101 #if '--no-default-filter' in str($filter_control.others): 101 #if '--no-default-filter' in str($filter_control.others):
102 && ln -s variants.vcf variants.vcf.gz 102 && ln -s variants.vcf variants.vcf.gz
103 && gzip -df variants.vcf.gz 103 && gzip -df variants.vcf.gz
104 #end if 104 #end if
105 #end if 105 #end if
106 && echo $filter_control.filter_type
106 ]]></command> 107 ]]></command>
107 <inputs> 108 <inputs>
108 <param type="data" name="reads" format="bam" label="Input reads in BAM format" /> 109 <param type="data" name="reads" format="bam" label="Input reads in BAM format" />
109 <expand macro="reference_interface" /> 110 <expand macro="reference_interface" />
110 <conditional name="regions"> 111 <conditional name="regions">
283 <tests> 284 <tests>
284 <test> 285 <test>
285 <param name="reads" ftype="bam" value="lofreq-in1.bam" /> 286 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
286 <param name="ref_selector" value="history" /> 287 <param name="ref_selector" value="history" />
287 <param name="ref" ftype="fasta" value="pBR322.fa" /> 288 <param name="ref" ftype="fasta" value="pBR322.fa" />
288 <output name="variants" file="call-out1.vcf" lines_diff="4" /> 289 <!-- lines_diff="4" should be sufficient, but https://github.com/CSB5/lofreq/issues/131 -->
290 <output name="variants" file="call-out1.vcf" lines_diff="6" />
291 <assert_command>
292 <has_text text="--sig 0.01"/>
293 <has_text text="--bonf dynamic"/>
294 <has_text text="--no-default-filter" negate="true"/>
295 </assert_command>
289 </test> 296 </test>
290 <test> 297 <test>
291 <param name="reads" ftype="bam" value="lofreq-in1.bam" /> 298 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
292 <param name="ref_selector" value="history" /> 299 <param name="ref_selector" value="history" />
293 <param name="ref" ftype="fasta" value="pBR322.fa" /> 300 <param name="ref" ftype="fasta" value="pBR322.fa" />
294 <conditional name="call_control"> 301 <conditional name="call_control">
295 <param name="set_call_options" value="yes" /> 302 <param name="set_call_options" value="yes" />
296 </conditional> 303 </conditional>
297 <output name="variants" file="call-out1.vcf" lines_diff="4" /> 304 <!-- lines_diff="4" should be sufficient, but https://github.com/CSB5/lofreq/issues/131 -->
305 <output name="variants" file="call-out1.vcf" lines_diff="6" />
298 </test> 306 </test>
299 <test> 307 <test>
300 <param name="reads" ftype="bam" value="lofreq-in1.bam" /> 308 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
301 <param name="ref_selector" value="history" /> 309 <param name="ref_selector" value="history" />
302 <param name="ref" ftype="fasta" value="pBR322.fa" /> 310 <param name="ref" ftype="fasta" value="pBR322.fa" />
308 <param name="def_nm_q" value="40" /> 316 <param name="def_nm_q" value="40" />
309 <param name="ign_vcf" ftype="vcf" value="call-out1.vcf" /> 317 <param name="ign_vcf" ftype="vcf" value="call-out1.vcf" />
310 </conditional> 318 </conditional>
311 </section> 319 </section>
312 </conditional> 320 </conditional>
313 <output name="variants" file="call-out1.vcf" lines_diff="4" /> 321 <!-- lines_diff="4" should be sufficient, but https://github.com/CSB5/lofreq/issues/131 -->
322 <output name="variants" file="call-out1.vcf" lines_diff="6" />
314 </test> 323 </test>
315 <test> 324 <test>
316 <param name="reads" ftype="bam" value="lofreq-in1.bam" /> 325 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
317 <param name="ref_selector" value="history" /> 326 <param name="ref_selector" value="history" />
318 <param name="ref" ftype="fasta" value="pBR322.fa" /> 327 <param name="ref" ftype="fasta" value="pBR322.fa" />