Mercurial > repos > jjohnson > snpeff
changeset 7:0ad9733e22a4
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 29 Nov 2013 09:27:22 -0500 |
| parents | eb394dd65c98 |
| children | aecbd8878923 |
| files | lib/galaxy/datatypes/snpeff.pyc snpEff.xml snpEff_download.xml snpEff_macros.xml snpSift_annotate.xml snpSift_caseControl.xml snpSift_filter.xml snpSift_int.xml |
| diffstat | 8 files changed, 335 insertions(+), 345 deletions(-) [+] |
line wrap: on
line diff
--- a/snpEff.xml Thu Nov 28 08:16:11 2013 -0600 +++ b/snpEff.xml Fri Nov 29 09:27:22 2013 -0500 @@ -1,72 +1,73 @@ <tool id="snpEff" name="SnpEff" version="3.4"> <description>Variant effect and annotation</description> - <requirements> - <requirement type="package" version="3.4">snpEff</requirement> - </requirements> + <expand macro="requirements" /> + <macros> + <import>snpEff_macros.xml</import> + </macros> <command> -java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff --c \$SNPEFF_JAR_PATH/snpEff.config --i $inputFormat -o $outputFormat -upDownStreamLen $udLength -#if $spliceSiteSize and $spliceSiteSize.__str__ != '': - -spliceSiteSize $spliceSiteSize -#end if -#if $filterIn and $filterIn.__str__ != 'no_filter': - $filterIn -#end if -#if $filterHomHet and $filterHomHet.__str__ != 'no_filter': - $filterHomHet -#end if -#if $annotations and $annotations.__str__ != '': - #echo " " - #echo ' '.join($annotations.__str__.split(',')) -#end if -#if $filterOut and $filterOut.__str__ != '': - #echo " " - #echo ' '.join($filterOut.__str__.split(',')) -#end if -#if str( $transcripts ) != 'None': - -onlyTr $transcripts -#end if -#if str( $intervals ) != 'None': ### fix this for multiple dataset input - -interval $intervals -#end if -#if $statsFile: - -stats $statsFile -#end if -#if $offset.__str__ != '': - ${offset} -#end if -#if $chr.__str__.strip() != '': - -chr "$chr" -#end if - $noLog -#if $snpDb.genomeSrc == 'cached': - -dataDir ${snpDb.genomeVersion.fields.path} - #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': - #echo " " - #echo ' '.join($snpDb.extra_annotations.__str__.split(',')) - #end if - #if $snpDb.regulation and $snpDb.regulation.__str__ != '': - -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# - #end if - $snpDb.genomeVersion -#elif $snpDb.genomeSrc == 'history': - -dataDir ${snpDb.snpeff_db.extra_files_path} - #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': - #set annotations = [' '] + $snpDb.extra_annotations.__str__.split(',') - #echo " " - #echo ' -'.join($annotations) - #end if - #if $snpDb.regulation and $snpDb.regulation.__str__ != '': - -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# - #end if - ${snpDb.snpeff_db.metadata.genome_version} -#else - -download - $snpDb.genome_version -#end if -$input > $snpeff_output -</command> + java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff + -c \$SNPEFF_JAR_PATH/snpEff.config + -i $inputFormat -o $outputFormat -upDownStreamLen $udLength + #if $spliceSiteSize and $spliceSiteSize.__str__ != '': + -spliceSiteSize $spliceSiteSize + #end if + #if $filterIn and $filterIn.__str__ != 'no_filter': + $filterIn + #end if + #if $filterHomHet and $filterHomHet.__str__ != 'no_filter': + $filterHomHet + #end if + #if $annotations and $annotations.__str__ != '': + #echo " " + #echo ' '.join($annotations.__str__.split(',')) + #end if + #if $filterOut and $filterOut.__str__ != '': + #echo " " + #echo ' '.join($filterOut.__str__.split(',')) + #end if + #if str( $transcripts ) != 'None': + -onlyTr $transcripts + #end if + #if str( $intervals ) != 'None': ### fix this for multiple dataset input + -interval $intervals + #end if + #if $statsFile: + -stats $statsFile + #end if + #if $offset.__str__ != '': + ${offset} + #end if + #if $chr.__str__.strip() != '': + -chr "$chr" + #end if + $noLog + #if $snpDb.genomeSrc == 'cached': + -dataDir ${snpDb.genomeVersion.fields.path} + #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': + #echo " " + #echo ' '.join($snpDb.extra_annotations.__str__.split(',')) + #end if + #if $snpDb.regulation and $snpDb.regulation.__str__ != '': + -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# + #end if + $snpDb.genomeVersion + #elif $snpDb.genomeSrc == 'history': + -dataDir ${snpDb.snpeff_db.extra_files_path} + #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': + #set annotations = [' '] + $snpDb.extra_annotations.__str__.split(',') + #echo " " + #echo ' -'.join($annotations) + #end if + #if $snpDb.regulation and $snpDb.regulation.__str__ != '': + -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# + #end if + ${snpDb.snpeff_db.metadata.genome_version} + #else + -download + $snpDb.genome_version + #end if + $input > $snpeff_output + </command> <inputs> <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> @@ -85,10 +86,10 @@ </param> <conditional name="snpDb"> - <param name="genomeSrc" type="select" label=""> - <option value="cached">Locally cached</option> - <option value="history">history</option> - <option value="named">named on demand</option> + <param name="genomeSrc" type="select" label="Genome source"> + <option value="cached">Locally installed reference genome</option> + <option value="history">Reference genome from your history</option> + <option value="named">Named on demand</option> </param> <when value="cached"> <param name="genomeVersion" type="select" label="Genome"> @@ -142,7 +143,7 @@ <option value="20000">20000 bases</option> </param> - <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases. Default: 2"> + <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases" help="Default: 2"> <option value="1">1 base</option> <option value="2">2 bases</option> <option value="3">3 bases</option> @@ -170,23 +171,23 @@ </param> <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options"> - <option value="-cancer">Perform 'cancer' comparissons (Somatic vs Germline). Default: false</option> - <option value="-canon">Only use canonical transcripts.</option> - <option value="-geneId">Use gene ID instead of gene name (VCF output). Default: false</option> - <option value="-hgvs">Use HGVS annotations for amino acid sub-field. Default: false</option> - <option value="-lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.</option> - <option value="-oicr">Add OICR tag in VCF file. Default: false</option> - <option value="-onlyReg">Only use regulation tracks.</option> - <option value="-sequenceOntolgy">Use Sequence Ontolgy terms. Default: false</option> + <option value="-cancer">Perform 'cancer' comparissons (Somatic vs Germline)</option> + <option value="-canon" selected="true">Only use canonical transcripts</option> + <option value="-geneId">Use gene ID instead of gene name (VCF output)</option> + <option value="-hgvs">Use HGVS annotations for amino acid sub-field</option> + <option value="-lof" selected="true">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags</option> + <option value="-oicr">Add OICR tag in VCF file</option> + <option value="-onlyReg" selected="true">Only use regulation tracks</option> + <option value="-sequenceOntolgy">Use Sequence Ontolgy terms.</option> </param> <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/> - <param name="transcripts" format="tabular" type="data" optional="true" label="Only use the transcripts in this file. Format: One transcript ID per line."/> + <param name="transcripts" format="tabular" type="data" optional="true" label="Only use the transcripts in this file." help="Format is one transcript ID per line."/> <param name="filterOut" type="select" display="checkboxes" multiple="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> + <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"> @@ -195,12 +196,11 @@ <option value="-1">Force one-based positions (both input and output)</option> </param> <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name"> - <help> - By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'. - You can prepend any string you want to the chromosome name." - </help> - <validator type="regex" message="No whitespace allows">^\S*$</validator> - + <help> + By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'. + You can prepend any string you want to the chromosome name. + </help> + <validator type="regex" message="No whitespace allowed">^\S*$</validator> </param> <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/> <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/> @@ -214,15 +214,11 @@ <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" /> - <exit_code range="-1" level="fatal" description="Error: Cannot open file" /> - </stdio> + <expand macro="stdio" /> <tests> <!-- Check that an effect was added in out VCF --> <!-- Check for a HTML header indicating that this was successful --> @@ -323,13 +319,9 @@ This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions. -For details about this tool, please go to http://snpEff.sourceforge.net +@EXTERNAL_DOCUMENTATION@ -SnpEff citation: -"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process] - -SnpSift citation: -"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012. +@CITATION_SECTION@ </help> </tool>
--- a/snpEff_download.xml Thu Nov 28 08:16:11 2013 -0600 +++ b/snpEff_download.xml Fri Nov 29 09:27:22 2013 -0500 @@ -1,14 +1,15 @@ <tool id="snpEff_download" name="SnpEff Download" version="3.4"> <description>Download a new database</description> - <requirements> - <requirement type="package" version="3.4">snpEff</requirement> - </requirements> + <expand macro="requirements" /> + <macros> + <import>snpEff_macros.xml</import> + </macros> <command> echo $genomeVersion > $snpeff_db; java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.extra_files_path -v $genomeVersion > $logfile </command> <inputs> - <param name="genomeVersion" type="select" label="Genome Version"> + <param name="genomeVersion" type="select" label="Select the genome version you want to download"> <options from_data_table="snpeff_databases"> <filter type="sort_by" column="0" /> </options> @@ -18,18 +19,12 @@ <data format="txt" name="logfile" /> <data format="snpeffdb" name="snpeff_db" label="${genomeVersion}" /> </outputs> - <stdio> - <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> - <exit_code range="1:" level="fatal" description="Error" /> - </stdio> + <expand macro="stdio" /> <help> -This tool downloads a SnpEff database into the users history for use by snpEff. +@EXTERNAL_DOCUMENTATION@ -For details about this tool, please go to http://snpEff.sourceforge.net - -Please cite: -"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process] +@CITATION_SECTION@ </help> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_macros.xml Fri Nov 29 09:27:22 2013 -0500 @@ -0,0 +1,45 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="3.4">snpEff</requirement> + </requirements> + </xml> + <xml name="stdio"> + <conditional name="analysis_param_type"> + <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options"> + <option value="basic" selected="True">Basic</option> + <option value="advanced">Advanced</option> + </param> + <when value="basic"> + <!-- Do nothing here --> + </when> + <when value="advanced"> + <yield /> + </when> + </conditional> + </xml> + <xml name="reference_source_selector_param"> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@EXTERNAL_DOCUMENTATION@"> + +For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals + + </token> + <token name="@CITATION_SECTION@">------ + +**Citation** + +For the underlying tool, please cite the following two publications: + +SnpEff citation: +"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process] + +SnpSift citation: +"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012. + + </token> +</macros>
--- a/snpSift_annotate.xml Thu Nov 28 08:16:11 2013 -0600 +++ b/snpSift_annotate.xml Fri Nov 29 09:27:22 2013 -0500 @@ -1,13 +1,13 @@ <tool id="snpSift_annotate" name="SnpSift Annotate" version="3.4"> - <description>Annotate SNPs from dbSnp</description> - <!-- - You will need to change the path to wherever your installation is. - You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) - --> - <requirements> - <requirement type="package" version="3.4">snpEff</requirement> - </requirements> - <command> + <description>SNPs from dbSnp</description> + <!-- + You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) + --> + <expand macro="requirements" /> + <macros> + <import>snpEff_macros.xml</import> + </macros> + <command> java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd #if $annotate.id : -id @@ -15,55 +15,49 @@ -info "$annotate.info_ids" #end if -q $dbSnp $input > $output - </command> - <inputs> - <param format="vcf" name="input" type="data" label="VCF input"/> - <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" - help="The ID field for a variant in input will be assigned from a matching variant in this file."/> - <conditional name="annotate"> - <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/> - <when value="id"/> - <when value="info"> - <param name="info_ids" type="text" value="" size="60" optional="true" label="Limit INFO annotation to these INFO IDs" - help="list is a comma separated list of fields. When blank, all INFO fields are included"> - <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> - </param> - </when> - </conditional> - <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Annotate in Memory"> - <help> - Allows unsorted VCF files, but it loads the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files). - Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). - </help> + </command> + <inputs> + <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> + <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" + help="The ID field for a variant in input will be assigned from a matching variant in this file."/> + <conditional name="annotate"> + <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/> + <when value="id"/> + <when value="info"> + <param name="info_ids" type="text" value="" size="60" optional="true" label="Limit INFO annotation to these INFO IDs" + help="list is a comma separated list of fields. When blank, all INFO fields are included"> + <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> </param> - </inputs> - <stdio> - <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> - <exit_code range="1:" level="fatal" description="Error" /> - </stdio> - - <outputs> - <data format="vcf" name="output" /> - </outputs> - <tests> - <test> - <param name="input" ftype="vcf" value="annotate_1.vcf"/> - <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/> - <param name="annotate_cmd" value="False"/> - <param name="id" value="True"/> - <output name="output"> - <assert_contents> - <has_text text="rs76166080" /> - </assert_contents> - </output> - </test> - </tests> - <help> + </when> + </conditional> + <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files"> + <help> + This option will load the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files). + Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). + </help> + </param> + </inputs> + <expand macro="stdio" /> + <outputs> + <data format="vcf" name="output" /> + </outputs> + <tests> + <test> + <param name="input" ftype="vcf" value="annotate_1.vcf"/> + <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/> + <param name="annotate_cmd" value="False"/> + <param name="id" value="True"/> + <output name="output"> + <assert_contents> + <has_text text="rs76166080" /> + </assert_contents> + </output> + </test> + </tests> + <help> This is typically used to annotate IDs from dbSnp. -For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#annotate - Annotatating only the ID field from dbSnp137.vcf :: Input VCF: @@ -95,13 +89,11 @@ 22 16350245 rs2905295 C A 0.0 FAIL NS=192;RSPOS=16350245;GMAF=0.230804387568556;dbSNPBuildID=101;SSR=1;SAO=0;VP=050000000000000100000140;WGT=0;VC=SNV;GNO -SnpEff citation: -"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process] +@EXTERNAL_DOCUMENTATION@ -SnpSift citation: -"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012. +@CITATION_SECTION@ - </help> + </help> </tool>
--- a/snpSift_caseControl.xml Thu Nov 28 08:16:11 2013 -0600 +++ b/snpSift_caseControl.xml Fri Nov 29 09:27:22 2013 -0500 @@ -1,13 +1,13 @@ <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.4"> - <description>Count samples are in 'case' and 'control' groups.</description> - <!-- - You will need to change the path to wherever your installation is. - You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) - --> - <requirements> - <requirement type="package" version="3.4">snpEff</requirement> - </requirements> - <command> + <description>Count samples are in 'case' and 'control' groups.</description> + <!-- + You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) + --> + <expand macro="requirements" /> + <macros> + <import>snpEff_macros.xml</import> + </macros> + <command> java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q #if $name.__str__.strip() != '': -name $name @@ -18,79 +18,73 @@ -tfam "$ctrl.tfam" #end if $input > $output - </command> - <inputs> - <param format="vcf" name="input" type="data" label="VCF input"/> - <conditional name="ctrl"> - <param name="ctrl_src" type="select" label="Case Control defined in"> - <option value="caseString">Case Control String</option> - <option value="tfam">TFAM</option> - </param> - <when value="caseString"> - <param name="caseControlStr" type="text" label="Case / Control column designation" size="50"> - <help> - Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral - </help> - <validator type="regex" message="must be only plus(+), minus(-), or zero(0) characters">[+-0]+</validator> + </command> + <inputs> + <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> + <conditional name="ctrl"> + <param name="ctrl_src" type="select" label="Case Control defined in"> + <option value="caseString">Case Control String</option> + <option value="tfam">TFAM file</option> </param> - </when> - <when value="tfam"> - <param format="tabular" name="tfam" type="data" label="PLINK TFAM file"/> - </when> - </conditional> - <param name="name" type="text" optional="true" label="name" help="name to append to the 'Cases' or 'Controls' tags"> - <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]+</validator> - </param> - </inputs> - <outputs> - <data format="vcf" name="output" /> - </outputs> - <stdio> - <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> - <exit_code range="1:" level="fatal" description="Error" /> - </stdio> - <tests> + <when value="caseString"> + <param name="caseControlStr" type="text" label="Case / Control column designation" size="50"> + <help> + Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral + </help> + <validator type="regex" message="must be only plus(+), minus(-), or zero(0) characters">[+-0]+</validator> + </param> + </when> + <when value="tfam"> + <param format="tabular" name="tfam" type="data" label="PLINK TFAM file" help="Read more about TFAM at http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#tr"/> + </when> + </conditional> + <param name="name" type="text" optional="true" label="name" help="name to append to the 'Cases' or 'Controls' tags"> + <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]+</validator> + </param> + </inputs> + <outputs> + <data format="vcf" name="output" /> + </outputs> + <expand macro="stdio" /> + <tests> + <test> + <param name="input" ftype="vcf" value="test.private.01.vcf"/> + <param name="ctrl_src" value="caseString"/> + <param name="caseControlStr" value="--"/> + <output name="output"> + <assert_contents> + <has_text text="Cases=0,0,0;" /> + <has_text text="Controls=0,0,0;" /> + </assert_contents> + </output> + </test> - <test> - <param name="input" ftype="vcf" value="test.private.01.vcf"/> - <param name="ctrl_src" value="caseString"/> - <param name="caseControlStr" value="--"/> - <output name="output"> - <assert_contents> - <has_text text="Cases=0,0,0;" /> - <has_text text="Controls=0,0,0;" /> - </assert_contents> - </output> - </test> + <test> + <param name="input" ftype="vcf" value="test.private.02.vcf"/> + <param name="ctrl_src" value="caseString"/> + <param name="caseControlStr" value="--"/> + <output name="output"> + <assert_contents> + <has_text text="Cases=0,0,0;" /> + <has_text text="Controls=2,0,4;" /> + </assert_contents> + </output> + </test> - <test> - <param name="input" ftype="vcf" value="test.private.02.vcf"/> - <param name="ctrl_src" value="caseString"/> - <param name="caseControlStr" value="--"/> - <output name="output"> - <assert_contents> - <has_text text="Cases=0,0,0;" /> - <has_text text="Controls=2,0,4;" /> - </assert_contents> - </output> - </test> - - <test> - <param name="input" ftype="vcf" value="test.private.02.vcf"/> - <param name="name" value=""/> - <param name="ctrl_src" value="caseString"/> - <param name="caseControlStr" value="-+"/> - <output name="output"> - <assert_contents> - <has_text text="Cases=1,0,2;" /> - <has_text text="Controls=1,0,2;" /> - </assert_contents> - </output> - </test> - - </tests> - - <help> + <test> + <param name="input" ftype="vcf" value="test.private.02.vcf"/> + <param name="name" value=""/> + <param name="ctrl_src" value="caseString"/> + <param name="caseControlStr" value="-+"/> + <output name="output"> + <assert_contents> + <has_text text="Cases=1,0,2;" /> + <has_text text="Controls=1,0,2;" /> + </assert_contents> + </output> + </test> + </tests> + <help> **SnpSift CaseControl** @@ -119,15 +113,9 @@ - Case / Control column designation = ""++++------" -For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol - -SnpEff citation: -"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process] +@EXTERNAL_DOCUMENTATION@ -SnpSift citation: -"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012. - - +@CITATION_SECTION@ </help> </tool>
--- a/snpSift_filter.xml Thu Nov 28 08:16:11 2013 -0600 +++ b/snpSift_filter.xml Fri Nov 29 09:27:22 2013 -0500 @@ -1,9 +1,10 @@ <tool id="snpSift_filter" name="SnpSift Filter" version="3.4"> <options sanitize="False" /> <description>Filter variants using arbitrary expressions</description> - <requirements> - <requirement type="package" version="3.4">snpEff</requirement> - </requirements> + <expand macro="requirements" /> + <macros> + <import>snpEff_macros.xml</import> + </macros> <command> java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse #if $filtering.mode == 'field': @@ -23,11 +24,11 @@ > $output </command> <inputs> - <param format="vcf" name="input" type="data" label="VCF input"/> - <param name="expr" type="text" label="Expression" size="160"/> - <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse. Show lines that do not match filter expression"/> + <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> + <param name="expr" type="text" label="Filter criteria" size="160" help="Need help? See below a few examples." /> + <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse filter" help="Show lines that do not match filter expression" /> <conditional name="filtering"> - <param name="mode" type="select" labael="Filter mode"> + <param name="mode" type="select" label="Filter mode"> <option value="entries" selected="true">Retain entries that pass filter, remove other entries</option> <option value="field">Change the FILTER field, but retain all entries</option> </param> @@ -56,13 +57,8 @@ <outputs> <data format="vcf" name="output" /> </outputs> - <stdio> - <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> - <exit_code range="1:" level="fatal" description="Error" /> - </stdio> - + <expand macro="stdio" /> <tests> - <test> <param name="input" ftype="vcf" value="test01.vcf"/> <param name="expr" value="QUAL >= 50"/> @@ -114,9 +110,7 @@ </assert_contents> </output> </test> - </tests> - <help> **SnpSift filter** @@ -146,14 +140,9 @@ * **isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] )** -For complete details about this tool and epressions that can be used, please go to http://snpeff.sourceforge.net/SnpSift.html#filter +@EXTERNAL_DOCUMENTATION@ -SnpEff citation: -"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process] - -SnpSift citation: -"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012. - +@CITATION_SECTION@ </help> </tool>
--- a/snpSift_int.xml Thu Nov 28 08:16:11 2013 -0600 +++ b/snpSift_int.xml Fri Nov 29 09:27:22 2013 -0500 @@ -1,67 +1,56 @@ <tool id="snpSift_int" name="SnpSift Intervals" version="3.4"> - <description>Filter variants using intervals </description> - <!-- - You will need to change the path to wherever your installation is. - You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) - --> - <requirements> - <requirement type="package" version="3.4">snpEff</requirement> - </requirements> - <command> - java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output - </command> - <inputs> - <param format="vcf" name="input" type="data" label="VCF input"/> - <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/> - <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals" - help="Filter out (exclude) VCF entries that match any interval in the BED files"/> - </inputs> - <outputs> - <data format="vcf" name="output" /> - </outputs> - <stdio> - <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> - <exit_code range="1:" level="fatal" description="Error" /> - </stdio> - <tests> + <description>Filter variants using intervals</description> + <!-- + You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) + --> + <expand macro="requirements" /> + <macros> + <import>snpEff_macros.xml</import> + </macros> + <command> + java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output + </command> + <inputs> + <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> + <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/> + <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals" + help="Filter out (exclude) VCF entries that match any interval in the BED files"/> + </inputs> + <outputs> + <data format="vcf" name="output" /> + </outputs> + <expand macro="stdio" /> + <tests> + <test> + <param name="input" ftype="vcf" value="annotate_5.vcf"/> + <param name="bedFile" ftype="bed" value="interval.bed"/> + <param name="exclude" value="False"/> + <output name="output"> + <assert_contents> + <has_text text="872687" /> + <not_has_text text="1195966" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" ftype="vcf" value="annotate_5.vcf"/> + <param name="bedFile" ftype="bed" value="interval.bed"/> + <param name="exclude" value="True"/> + <output name="output"> + <assert_contents> + <has_text text="1195966" /> + <not_has_text text="872687" /> + </assert_contents> + </output> + </test> + </tests> + <help> - <test> - <param name="input" ftype="vcf" value="annotate_5.vcf"/> - <param name="bedFile" ftype="bed" value="interval.bed"/> - <param name="exclude" value="False"/> - <output name="output"> - <assert_contents> - <has_text text="872687" /> - <not_has_text text="1195966" /> - </assert_contents> - </output> - </test> +You can filter using intervals (BED file). + +@EXTERNAL_DOCUMENTATION@ - <test> - <param name="input" ftype="vcf" value="annotate_5.vcf"/> - <param name="bedFile" ftype="bed" value="interval.bed"/> - <param name="exclude" value="True"/> - <output name="output"> - <assert_contents> - <has_text text="1195966" /> - <not_has_text text="872687" /> - </assert_contents> - </output> - </test> - - </tests> +@CITATION_SECTION@ - <help> - -You can filter using intervals (BED file) - -For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals - -SnpEff citation: -"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process] - -SnpSift citation: -"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012. - - </help> + </help> </tool>