Mercurial > repos > jjohnson > snpeff
diff snpEff.xml @ 18:36f3c82323e6
Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 13 Jan 2015 13:36:11 -0600 |
| parents | 13d81e5226cd |
| children | 2e37b58fc24d |
line wrap: on
line diff
--- a/snpEff.xml Mon Nov 10 09:33:36 2014 -0600 +++ b/snpEff.xml Tue Jan 13 13:36:11 2015 -0600 @@ -1,13 +1,14 @@ -<tool id="snpEff" name="SnpEff" version="4.0.1"> +<tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.2"> <description>Variant effect and annotation</description> <expand macro="requirements" /> <macros> <import>snpEff_macros.xml</import> </macros> <command> +<![CDATA[ java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config - -i $inputFormat -o $outputFormat -upDownStreamLen $udLength + -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength #if $spliceSiteSize and $spliceSiteSize.__str__ != '': -spliceSiteSize $spliceSiteSize #end if @@ -32,7 +33,7 @@ -interval $intervals #end if #if $statsFile: - -stats snpeff_report + -stats $statsFile #end if #if $offset.__str__ != 'default': ${offset} @@ -66,10 +67,19 @@ -download $snpDb.genome_version #end if - $input > $snpeff_output + $input > $snpeff_output ; #if $statsFile: - && mkdir $statsFile.extra_files_path && cp snpeff_report.genes.txt $statsFile.extra_files_path + #import os + #set $genes_file = str($statsFile) + '.genes.txt' + #set $genes_file_name = os.path.split($genes_file)[-1] + mkdir $statsFile.files_path; + mv $genes_file #echo os.path.join($statsFile.files_path, $genes_file_name)#; #end if + #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1 + ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]" + sed -i 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output + #end if +]]> </command> <inputs> <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> @@ -81,12 +91,22 @@ <option value="bed">BED (Deprecated)</option> </param> - <param name="outputFormat" type="select" label="Output format"> - <option value="vcf" selected="true">VCF (only if input is VCF)</option> - <option value="txt">Tabular</option> - <option value="bed">BED</option> - <option value="bedAnn">BED Annotations</option> - </param> + <conditional name="outputConditional"> + <param name="outputFormat" type="select" label="Output format"> + <option value="vcf" selected="true">VCF (only if input is VCF)</option> + <option value="gatk">GATK-compatible VCF (only if input is VCF)</option> + <option value="txt">Tabular</option> + <option value="bed">BED</option> + <option value="bedAnn">BED annotations</option> + </param> + <when value="vcf" /> + <when value="gatk"> + <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" /> + </when> + <when value="txt" /> + <when value="bed" /> + <when value="bedAnn" /> + </conditional> <conditional name="snpDb"> <param name="genomeSrc" type="select" label="Genome source"> @@ -97,35 +117,36 @@ <when value="cached"> <param name="genomeVersion" type="select" label="Genome"> <!--GENOME DESCRIPTION--> - <options from_data_table="snpeff4_genomedb"> - <filter type="unique_value" column="0" /> + <options from_data_table="snpeffv_genomedb"> + <filter type="static_value" name="snpeff_version" value="SnpEff4.1" column="1"/> + <filter type="unique_value" column="2" /> </options> </param> - <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations"> + <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations"> <help>These are available for only a few genomes</help> - <options from_data_table="snpeff4_annotations"> - <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> + <options from_data_table="snpeffv_annotations"> + <filter type="param_value" ref="genomeVersion" key="genome" column="2" /> <filter type="unique_value" column="1" /> </options> </param> - <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory Annotation"> + <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation"> <help>These are available for only a few genomes</help> - <options from_data_table="snpeff4_regulationdb"> - <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> + <options from_data_table="snpeffv_regulationdb"> + <filter type="param_value" ref="genomeVersion" key="genome" column="2" /> <filter type="unique_value" column="1" /> </options> </param> </when> <when value="history"> - <param format="snpeffdbv4" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/> + <param format="snpeffdbv41" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/> <!-- From metadata --> - <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations"> + <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations"> <help>These are available for only a few genomes</help> <options> <filter type="data_meta" ref="snpeff_db" key="annotation" /> </options> </param> - <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory Annotation"> + <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation"> <help>These are available for only a few genomes</help> <options> <filter type="data_meta" ref="snpeff_db" key="regulation" /> @@ -134,7 +155,7 @@ </when> <when value="named"> <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> - <help>http://sourceforge.net/projects/snpeff/files/databases/v4_0/</help> + <help>@SNPEFF_DATABASE_URL@</help> <validator type="regex" message="A genome version name is required">\S+</validator> </param> </when> @@ -153,7 +174,7 @@ <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="2" selected="true">2 bases</option> <option value="3">3 bases</option> <option value="4">4 bases</option> <option value="5">5 bases</option> @@ -165,24 +186,24 @@ <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes"> <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> + <option value="-hom">Analyze homozygous sequence changes only</option> + <option value="-het">Analyze heterozygous sequence changes only</option> </param> <!-- The tool testing code can not handle select,radio,check boxes values that start with '-', so the '-' is added in the command generation --> <param name="filterIn" type="select" display="radio" label="Filter sequence changes"> <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="-mnp">Only MNPs (multiple nucleotide polymorphisms) </option> - <option value="-snp">Only SNPs (single nucleotide polymorphisms) </option> + <option value="-del">Analyze deletions only</option> + <option value="-ins">Analyze insertions only</option> + <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms)</option> + <option value="-snp">Only SNPs (single nucleotide polymorphisms)</option> </param> <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options"> - <option value="-cancer">Perform 'cancer' comparissons (Somatic vs Germline)</option> + <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option> <option value="-canon">Only use canonical transcripts</option> <option value="-geneId">Use gene ID instead of gene name (VCF output)</option> - <option value="-lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags</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</option> <option value="-onlyReg">Only use regulation tracks</option> <option value="-classic">Use Classic Effect names and amino acid variant annotations (NON_SYNONYMOUS_CODING vs missense_variant and G180R vs p.Gly180Arg/c.538G>C)</option> @@ -217,13 +238,12 @@ <outputs> <data format="vcf" name="snpeff_output" > <change_format> - <when input="outputFormat" value="vcf" format="vcf" /> - <when input="outputFormat" value="txt" format="tabular" /> - <when input="outputFormat" value="bed" format="bed" /> - <when input="outputFormat" value="bedAnn" format="bed" /> + <when input="outputConditional.outputFormat" value="txt" format="tabular" /> + <when input="outputConditional.outputFormat" value="bed" format="bed" /> + <when input="outputConditional.outputFormat" value="bedAnn" format="bed" /> </change_format> </data> - <data format="html" name="statsFile" label="{tool.name} on ${on_string} Summary Report" from_work_dir="snpeff_report"> + <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats"> <filter>generate_stats == True</filter> </data> </outputs> @@ -287,7 +307,7 @@ <param name="genome_version" value="testCase"/> <param name="udLength" value="0"/> <param name="filterHomHet" value="no_filter"/> - <param name="filterIn" value="del"/> + <param name="filterIn" value="+-del"/> <!-- <param name="filterOut" value=""/> --> @@ -333,5 +353,6 @@ @CITATION_SECTION@ </help> + <expand macro="citations" /> </tool>