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comparison snpEff.xml @ 26:5b80f544c67f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51
author iuc
date Fri, 25 Nov 2022 19:44:27 +0000
parents 8f92c2b26e6d
children 6322be79bd8e
comparison
equal deleted inserted replaced
25:5c7b70713fb5 26:5b80f544c67f
1 <tool id="snpEff" name="SnpEff eff:" version="@WRAPPER_VERSION@.galaxy1"> 1 <tool id="snpEff" name="SnpEff eff:" version="@WRAPPER_VERSION@.galaxy2">
2 <description> annotate variants</description> 2 <description> annotate variants</description>
3 <macros> 3 <macros>
4 <import>snpEff_macros.xml</import> 4 <import>snpEff_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <expand macro="requirement" /> 7 <expand macro="requirement" />
8 </requirements> 8 </requirements>
9 <expand macro="stdio" /> 9 <expand macro="stdio" />
10 <expand macro="version_command" /> 10 <expand macro="version_command" />
11 <command><![CDATA[ 11 <command><![CDATA[
12 #if $intervals
13 ln -s '${intervals}' intervals.bed &&
14 #end if
12 snpEff @JAVA_OPTIONS@ eff 15 snpEff @JAVA_OPTIONS@ eff
13 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength 16 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
14 #if $spliceSiteSize and str($spliceSiteSize) != '': 17 #if $spliceSiteSize and str($spliceSiteSize) != '':
15 -spliceSiteSize "$spliceSiteSize" 18 -spliceSiteSize "$spliceSiteSize"
16 #end if 19 #end if
40 #end if 43 #end if
41 #if $transcripts 44 #if $transcripts
42 -onlyTr '$transcripts' 45 -onlyTr '$transcripts'
43 #end if 46 #end if
44 #if $intervals ### fix this for multiple dataset input 47 #if $intervals ### fix this for multiple dataset input
45 -interval '$intervals' 48 -interval intervals.bed
46 #end if 49 #end if
47 #if $statsFile: 50 #if $statsFile:
48 -stats '$statsFile' 51 -stats '$statsFile'
49 #end if 52 #end if
50 #if $csvStats: 53 #if $csvStats:
381 <has_text_matching expression="KJ660346\t572\t.*missense_variant" /> 384 <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
382 <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" /> 385 <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
383 </assert_contents> 386 </assert_contents>
384 </output> 387 </output>
385 </test> 388 </test>
389 <!-- Test interval option-->
390 <test>
391 <param name="input" ftype="vcf" value="input.vcf"/>
392 <param name="inputFormat" value="vcf"/>
393 <param name="outputFormat" value="vcf"/>
394 <param name="genomeSrc" value="named"/>
395 <param name="interval" value="intervals.bed"/>
396 <param name="genome_version" value="ebola_zaire"/>
397 <param name="udLength" value="0"/>
398 <param name="generate_stats" value="false"/>
399 <output name="snpeff_output">
400 <assert_contents>
401 <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
402 <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
403 </assert_contents>
404 </output>
405 </test>
386 </tests> 406 </tests>
387 <help><![CDATA[ 407 <help><![CDATA[
388 **What it does** 408 **What it does**
389 409
390 SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). 410 SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).