Mercurial > repos > jjohnson > snpeff
diff snpEff.xml @ 7:b26a1aff7f81
Fix issues with snpEff commandline template and add test cases
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 28 Mar 2013 12:29:45 -0500 |
| parents | 3b0c657b852b |
| children | 13b6ad2ddace |
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--- a/snpEff.xml Tue Mar 26 15:24:30 2013 -0500 +++ b/snpEff.xml Thu Mar 28 12:29:45 2013 -0500 @@ -13,7 +13,24 @@ eval "if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ; then java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion ; fi"; -java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command> +java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength +#if $filterIn and $filterIn.__str__ != 'no_filter': + -$filterIn +#end if +#if $filterHomHet and $filterHomHet.__str__ != 'no_filter': + -$filterHomHet +#end if +#if $filterOut and $filterOut.__str__ != '': + #echo ' '.join($filterOut.__str__.split(',')) +#end if +#if $statsFile: + -stats $statsFile +#end if +#if $offset.__str__ != '': + -${offset} +#end if + $genomeVersion $input > $snpeff_output +</command> <inputs> <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> @@ -50,36 +67,36 @@ </param> <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes"> - <option value="">No filter (analyze everything)</option> - <option value="-hom">Analyze homozygous sequence changes only </option> - <option value="-het">Analyze heterozygous sequence changes only </option> + <option value="no_filter" selected="true">No filter (analyze everything)</option> + <option value="hom">Analyze homozygous sequence changes only </option> + <option value="het">Analyze heterozygous sequence changes only </option> </param> <param name="filterIn" type="select" display="radio" label="Filter sequence changes"> - <option value="">No filter (analyze everything)</option> - <option value="-del">Analyze deletions only </option> - <option value="-ins">Analyze insertions only </option> - <option value="-nmp">Only MNPs (multiple nucleotide polymorphisms) </option> - <option value="-snp">Only SNPs (single nucleotide polymorphisms) </option> + <option value="no_filter" selected="true">No filter (analyze everything)</option> + <option value="del">Analyze deletions only </option> + <option value="ins">Analyze insertions only </option> + <option value="nmp">Only MNPs (multiple nucleotide polymorphisms) </option> + <option value="snp">Only SNPs (single nucleotide polymorphisms) </option> </param> - <param name="filterOut" type="select" display="checkboxes" multiple="true" optional="false" value="None" label="Filter output"> - <option value="None" selected="true">None</option> - <option value="downstream">Do not show DOWNSTREAM changes </option> - <option value="intergenic">Do not show INTERGENIC changes </option> - <option value="intron">Do not show INTRON changes </option> - <option value="upstream">Do not show UPSTREAM changes </option> - <option value="utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option> + <param name="filterOut" type="select" display="checkboxes" multiple="true" optional="true" label="Filter output"> + <option value="-no-downstream">Do not show DOWNSTREAM changes </option> + <option value="-no-intergenic">Do not show INTERGENIC changes </option> + <option value="-no-intron">Do not show INTRON changes </option> + <option value="-no-upstream">Do not show UPSTREAM changes </option> + <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option> </param> <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position"> - <option value="">Use default (based on input type)</option> - <option value="-0">Force zero-based positions (both input and output)</option> - <option value="-1">Force one-based positions (both input and output)</option> + <option value="" selected="true">Use default (based on input type)</option> + <option value="0">Force zero-based positions (both input and output)</option> + <option value="1">Force one-based positions (both input and output)</option> </param> + <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/> </inputs> <outputs> - <data format="tabular" name="output" > + <data format="tabular" name="snpeff_output" > <change_format> <when input="outputFormat" value="txt" format="tabular" /> <when input="outputFormat" value="vcf" format="vcf" /> @@ -87,12 +104,97 @@ <when input="outputFormat" value="bedAnn" format="bed" /> </change_format> </data> - <data format="html" name="statsFile" /> + + <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"/> + <param name="filterHomHet" value="no_filter"/> + <param name="filterIn" value="no_filter"/> + <param name="filterOut" value="-no-upstream"/> + <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> + <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"/> + <param name="filterHomHet" value="het"/> + <param name="filterIn" value="no_filter"/> + <!-- + <param name="filterOut" value=""/> + --> + <param name="generate_stats" value="False"/> + <output name="snpeff_output"> + <assert_contents> + <!-- Check that NO effects were added since -het is set --> + <not_has_text text="EFF=NON_SYNONYMOUS_CODING" /> + </assert_contents> + </output> + </test> + <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"/> + <param name="filterHomHet" value="no_filter"/> + <param name="filterIn" value="del"/> + <!-- + <param name="filterOut" value=""/> + --> + <param name="generate_stats" value="False"/> + <output name="snpeff_output"> + <assert_contents> + <!-- Check that deleletions were evaluated --> + <has_text_matching expression="Y\t59030478\t.*EFF=INTERGENIC" /> + <!-- Check that insertion on last line was NOT evaluated --> + <has_text_matching expression="Y\t59032947\t.*SF=5\tGT" /> + </assert_contents> + </output> + </test> + <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"/> + <param name="filterHomHet" value="no_filter"/> + <param name="filterIn" value="no_filter"/> + <param name="filterOut" value="-no-upstream"/> + <param name="generate_stats" value="False"/> + <output name="snpeff_output"> + <assert_contents> + <!-- Check that NO UPSTREAM effect was added --> + <not_has_text text="UPSTREAM" /> + </assert_contents> + </output> + </test> + + </tests> <help> This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.