Mercurial > repos > takakoron > snpeff_3_6c
diff snpEff_docker.xml @ 0:0d895b0e0f15 draft
planemo upload
| author | takakoron |
|---|---|
| date | Mon, 11 Apr 2016 11:16:50 -0400 |
| parents | |
| children | 216d02ec973a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_docker.xml Mon Apr 11 11:16:50 2016 -0400 @@ -0,0 +1,107 @@ +<tool id="snpEff_docker" name="SnpEff" version="3.6c (build 2014-05-20)"> + <description>Variant effect and annotation (Docker)</description> + <requirements> + <container type="docker">takakoron/snpeff_3.6c</container> + </requirements> + <command interpreter="perl">/usr/src/myapp/snpEffWrapper.pl eff +-i $inputFormat +-o $outputFormat +-upDownStreamLen $udLength +$canon +$hgvs +$lof +$motif +#if $statsFile: + -stats $statsFile +#end if + $genomeVersion $input > $snpeff_output +</command> + <inputs> + <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> + + <param name="inputFormat" type="select" label="Input format"> + <option value="vcf" selected="true">VCF</option> + <option value="txt">Tabular</option> + <option value="bed">BED</option> + </param> + + <param name="outputFormat" type="select" label="Output format"> + <option value="vcf" selected="true">VCF</option> + <option value="txt">Tabular</option> + <option value="bed">BED</option> + <option value="bedAnn">BED Annotations</option> + <option value="gatk">VCF (GATK compatible)</option> + </param> + + <param name="genomeVersion" type="select" label="Genome" help="If your annotation of interest is not listed, contact the P-GALAXY team (pipeline_dev@ddbj.nig.ac.jp)"> + <options from_file="snpEff_genomes.loc"> + <column name="name" index="1"/> + <column name="value" index="0"/> + </options> + </param> + + <param name="udLength" type="select" label="Upstream / Downstream length"> + <option value="0">No upstream / downstream intervals (0 bases)</option> + <option value="200">200 bases</option> + <option value="500">500 bases</option> + <option value="1000">1000 bases</option> + <option value="2000">2000 bases</option> + <option value="5000" selected="true">5000 bases</option> + <option value="10000">10000 bases</option> + <option value="20000">20000 bases</option> + </param> + + <param name="canon" type="boolean" truevalue="-canon" falsevalue="" checked="false" label="Use only cannonical transcripts"/> + <param name="hgvs" type="boolean" truevalue="-hgvs" falsevalue="" checked="false" label="Annotate using HGVS nomenclature"/> + <param name="lof" type="boolean" truevalue="-lof" falsevalue="" checked="false" label="Annotate Loss of function (LOF) and Nonsense mediated decay (NMD)"/> + <param name="motif" type="boolean" truevalue="-motif" falsevalue="" checked="false" label="Annotate transcription factor binding site motifs (only available for latest GRCh37)"/> + <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/> + </inputs> + <outputs> + <data format="tabular" name="snpeff_output" > + <change_format> + <when input="outputFormat" value="txt" format="tabular" /> + <when input="outputFormat" value="vcf" format="vcf" /> + <when input="outputFormat" value="bed" format="bed" /> + <when input="outputFormat" value="bedAnn" format="bed" /> + </change_format> + </data> + + <data format="html" name="statsFile"> + <filter>generate_stats == True</filter> + </data> + </outputs> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + <tests> + <test> + <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> + <param name="inputFormat" value="vcf"/> + <param name="outputFormat" value="vcf"/> + <param name="genomeVersion" value="testCase"/> + <param name="udLength" value="0"/> + <output name="snpeff_output"> + <assert_contents> + <!-- Check that an effect was added --> + <has_text text="EFF=NON_SYNONYMOUS_CODING" /> + </assert_contents> + </output> + <output name="statsFile"> + <assert_contents> + <!-- Check for a HTML header indicating that this was successful --> + <has_text text="SnpEff: Variant analysis" /> + </assert_contents> + </output> + </test> + </tests> + <help> + +This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions. + +For details about this tool, please go to http://snpEff.sourceforge.net + + </help> +</tool> +