Mercurial > repos > iuc > snpeff
changeset 26:5b80f544c67f draft
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 | 5c7b70713fb5 |
| children | 9473cd297a76 |
| files | snpEff.xml test-data/intervals.bed |
| diffstat | 2 files changed, 24 insertions(+), 2 deletions(-) [+] |
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--- a/snpEff.xml Wed Aug 03 16:33:45 2022 +0000 +++ b/snpEff.xml Fri Nov 25 19:44:27 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="snpEff" name="SnpEff eff:" version="@WRAPPER_VERSION@.galaxy1"> +<tool id="snpEff" name="SnpEff eff:" version="@WRAPPER_VERSION@.galaxy2"> <description> annotate variants</description> <macros> <import>snpEff_macros.xml</import> @@ -9,6 +9,9 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ + #if $intervals + ln -s '${intervals}' intervals.bed && + #end if snpEff @JAVA_OPTIONS@ eff -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength #if $spliceSiteSize and str($spliceSiteSize) != '': @@ -42,7 +45,7 @@ -onlyTr '$transcripts' #end if #if $intervals ### fix this for multiple dataset input - -interval '$intervals' + -interval intervals.bed #end if #if $statsFile: -stats '$statsFile' @@ -383,6 +386,23 @@ </assert_contents> </output> </test> + <!-- Test interval option--> + <test> + <param name="input" ftype="vcf" value="input.vcf"/> + <param name="inputFormat" value="vcf"/> + <param name="outputFormat" value="vcf"/> + <param name="genomeSrc" value="named"/> + <param name="interval" value="intervals.bed"/> + <param name="genome_version" value="ebola_zaire"/> + <param name="udLength" value="0"/> + <param name="generate_stats" value="false"/> + <output name="snpeff_output"> + <assert_contents> + <has_text_matching expression="KJ660346\t572\t.*missense_variant" /> + <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ **What it does**