| Previous changeset 2:e09ce114d240 (2016-02-19) Next changeset 4:698ef30638a8 (2016-09-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 |
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modified:
snpEff.xml snpEff_databases.xml snpEff_download.xml snpEff_macros.xml tool_dependencies.xml |
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removed:
repository_dependencies.xml |
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| diff -r e09ce114d240 -r b24873564cf6 repository_dependencies.xml --- a/repository_dependencies.xml Fri Feb 19 08:26:25 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="This requires the SnpEff datatype definitions."> - <repository name="snpeff_datatypes" owner="iuc" changeset_revision="d78b2b2a3388" toolshed="http://toolshed.g2.bx.psu.edu" /> -</repositories> |
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| diff -r e09ce114d240 -r b24873564cf6 snpEff.xml --- a/snpEff.xml Fri Feb 19 08:26:25 2016 -0500 +++ b/snpEff.xml Tue Jun 07 10:03:17 2016 -0400 |
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| @@ -1,11 +1,11 @@ <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.0"> <description>Variant effect and annotation</description> - <expand macro="requirements" /> <macros> <import>snpEff_macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> + <expand macro="version_command" /> <command> <![CDATA[ java -Xmx6G -jar "\$SNPEFF_JAR_PATH/snpEff.jar" eff @@ -14,6 +14,17 @@ #if $spliceSiteSize and str($spliceSiteSize) != '': -spliceSiteSize "$spliceSiteSize" #end if + #if $spliceRegion.setSpliceRegions == 'yes': + #if $spliceRegion.spliceRegionExonSize and str($spliceRegion.spliceRegionExonSize) != '': + -spliceRegionExonSize $spliceRegion.spliceRegionExonSize + #end if + #if $spliceRegion.spliceRegionIntronMin and str($spliceRegion.spliceRegionIntronMin) != '': + -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin + #end if + #if $spliceRegion.spliceRegionIntronMax and str($spliceRegion.spliceRegionIntronMax) != '': + -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax + #end if + #end if #if $annotations and str($annotations) != '': #echo " " #echo ' '.join(str($annotations).split(',')) @@ -87,8 +98,6 @@ <param name="inputFormat" type="select" label="Input format"> <option value="vcf" selected="true">VCF</option> - <option value="txt">Tabular (Deprecated)</option> - <option value="pileup">Pileup (Deprecated)</option> <option value="bed">BED (Deprecated)</option> </param> @@ -96,7 +105,6 @@ <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> @@ -104,7 +112,6 @@ <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> @@ -190,6 +197,19 @@ <option value="9">9 bases</option> </param> + <conditional name="spliceRegion"> + <param name="setSpliceRegions" type="select" label="spliceRegion Settings"> + <option value="no">Use Defaults</option> + <option value="yes">Set Splice Region Parameters</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="spliceRegionExonSize" type="integer" value="" min="1" max="10" optional="true" label="Set size for splice site region within exons. Default: 3 bases"/> + <param name="spliceRegionIntronMin" type="integer" value="" min="1" max="10" optional="true" label="Set minimum number of bases for splice site region within intron. Default: 3 bases"/> + <param name="spliceRegionIntronMax" type="integer" value="" min="1" max="10" optional="true" label="Set maximum number of bases for splice site region within intron. Default: 8 bases"/> + </when> + </conditional> + <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options"> <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option> <option value="-canon">Only use canonical transcripts</option> @@ -200,7 +220,13 @@ <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> <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option> <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option> + <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN').</option> + <option value="-noHgvs">Do not add HGVS annotations.</option> + <option value="-noLof">Do not add LOF and NMD annotations.</option> + <option value="-noShiftHgvs">Do not shift variants according to HGVS notation (most 3prime end).</option> + <option value="-oicr">Add OICR tag in VCF file. Default: false</option> </param> + <!-- -cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples. --> <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." help="Format is one transcript ID per line."/> <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output"> @@ -278,12 +304,11 @@ <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"/> + <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server"/> </inputs> <outputs> <data format="vcf" name="snpeff_output" > <change_format> - <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> @@ -301,7 +326,7 @@ <has_text text="SnpEff: Variant analysis" /> </assert_contents> </output> - --> + --> <!-- Setting filterOut throws exception in twilltestcase.py <test> <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> @@ -318,7 +343,7 @@ </assert_contents> </output> </test> - --> + --> <test> <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> @@ -361,14 +386,13 @@ --> </tests> - <help> + <help><![CDATA[ This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions. @EXTERNAL_DOCUMENTATION@ -@CITATION_SECTION@ - +]]> </help> <expand macro="citations" /> </tool> |
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| diff -r e09ce114d240 -r b24873564cf6 snpEff_databases.xml --- a/snpEff_databases.xml Fri Feb 19 08:26:25 2016 -0500 +++ b/snpEff_databases.xml Tue Jun 07 10:03:17 2016 -0400 |
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| @@ -1,12 +1,14 @@ <tool id="snpEff_databases" name="SnpEff Available Databases" version="@WRAPPER_VERSION@.0"> <description></description> - <expand macro="requirements" /> <macros> <import>snpEff_macros.xml</import> </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> <command> <![CDATA[ - java -jar \$SNPEFF_JAR_PATH/snpEff.jar databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g' > $snpeff_dbs + java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g' > "$snpeff_dbs" ]]> </command> <inputs> @@ -14,13 +16,21 @@ <outputs> <data format="tabular" name="snpeff_dbs" label="${tool.name} @SNPEFF_VERSION@ available databases" /> </outputs> - <expand macro="stdio" /> - <help> + <tests> + <test> + <output name="snpeff_dbs"> + <assert_contents> + <has_text text="ebola_zaire" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ @EXTERNAL_DOCUMENTATION@ -@CITATION_SECTION@ - +]]> </help> + <expand macro="citations" /> </tool> |
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| diff -r e09ce114d240 -r b24873564cf6 snpEff_download.xml --- a/snpEff_download.xml Fri Feb 19 08:26:25 2016 -0500 +++ b/snpEff_download.xml Tue Jun 07 10:03:17 2016 -0400 |
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| @@ -1,16 +1,18 @@ <tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.0"> <description>Download a new database</description> - <expand macro="requirements" /> <macros> <import>snpEff_macros.xml</import> </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> <command> <![CDATA[ - java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.files_path -v $genome_version + java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" download -c "\$SNPEFF_JAR_PATH/snpEff.config" -dataDir "$snpeff_db.files_path" -v "$genome_version" ]]> </command> <inputs> - <param name="genome_version" type="text" size="40" value="" label="Select the genome version you want to download (e.g. GRCh37.74)"> + <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh37.74)"> <help>@SNPEFF_DATABASE_URL@</help> <validator type="regex" message="A genome version name is required">\S+</validator> </param> @@ -18,13 +20,21 @@ <outputs> <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" /> </outputs> - <expand macro="stdio" /> - <help> + <tests> + <test> + <param name="genome_version" value="ebola_zaire"/> + <output name="snpeff_db"> + <assert_contents> + <has_text text="ebola_zaire" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ @EXTERNAL_DOCUMENTATION@ -@CITATION_SECTION@ - +]]> </help> <expand macro="citations" /> </tool> |
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| diff -r e09ce114d240 -r b24873564cf6 snpEff_macros.xml --- a/snpEff_macros.xml Fri Feb 19 08:26:25 2016 -0500 +++ b/snpEff_macros.xml Tue Jun 07 10:03:17 2016 -0400 |
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| @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="4.0">snpEff</requirement> + <requirement type="package" version="4.1">snpEff</requirement> </requirements> </xml> <xml name="stdio"> @@ -10,9 +10,12 @@ <exit_code range="1:" level="fatal" description="Error" /> </stdio> </xml> - <token name="@WRAPPER_VERSION@">4.0</token> - <token name="@SNPEFF_VERSION@">SnpEff4.0</token> - <token name="@SNPEFF_DATABASE_URL@">https://snpeff-data.galaxyproject.org/databases/v4_0/</token> + <xml name="version_command"> + <version_command>java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version</version_command> + </xml> + <token name="@WRAPPER_VERSION@">4.1</token> + <token name="@SNPEFF_VERSION@">SnpEff4.1</token> + <token name="@SNPEFF_DATABASE_URL@">https://snpeff-data.galaxyproject.org/databases/v4_1/</token> <token name="@EXTERNAL_DOCUMENTATION@"> For details about this tool, please go to: |
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| diff -r e09ce114d240 -r b24873564cf6 tool_dependencies.xml --- a/tool_dependencies.xml Fri Feb 19 08:26:25 2016 -0500 +++ b/tool_dependencies.xml Tue Jun 07 10:03:17 2016 -0400 |
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| @@ -1,7 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="snpEff" version="4.0"> - <repository name="package_snpeff_4_0" owner="iuc" changeset_revision="6bc55957927b" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="snpEff" version="4.1"> + <repository changeset_revision="374c7f8421fb" name="package_snpeff_4_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> - |