Mercurial > repos > iuc > lofreq_call
comparison lofreq_call.xml @ 7:66345032017a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2
| author | iuc |
|---|---|
| date | Wed, 06 Jul 2022 09:22:39 +0000 |
| parents | 90f5937da8a1 |
| children | 3116e6e4a934 |
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| 6:90f5937da8a1 | 7:66345032017a |
|---|---|
| 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" /> |