snpeff: snpEff.xml comparison

comparison snpEff.xml @ 3:b24873564cf6 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31

author	iuc
date	Tue, 07 Jun 2016 10:03:17 -0400
parents	e09ce114d240
children	698ef30638a8

comparison

equal deleted inserted replaced

-:e09ce114d240
+:b24873564cf6
 <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
 -c "\$SNPEFF_JAR_PATH/snpEff.config"
 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
 #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(','))
 #end if
 #if $filterOut and str($filterOut) != '':
 <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 (Deprecated)</option>
-<option value="pileup">Pileup (Deprecated)</option>
 <option value="bed">BED (Deprecated)</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">
 <option value="7">7 bases</option>
 <option value="8">8 bases</option>
 <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>
 <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="-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>
 <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>
-</param>
+<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">
 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
 <option value="-no-intergenic">Do not show INTERGENIC changes</option>
 You can prepend any string you want to the chromosome name.
 </help>
 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
 </param>
 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/>
-<param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/>
+<param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server"/>
 </inputs>
 <outputs>
 <data format="vcf" name="snpeff_output" >
 <change_format>
-<when input="outputConditional.outputFormat" value="txt" format="tabular" />
 <when input="outputConditional.outputFormat" value="bed" format="bed" />
 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
 </change_format>
 </data>
 <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats">
 <output name="statsFile">
 <assert_contents>
 <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"/>
 <param name="inputFormat" value="vcf"/>
 <param name="outputFormat" value="vcf"/>
 <assert_contents>
 <has_text text="EFF=" />
 </assert_contents>
 </output>
 </test>
 -->
 <test>
 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
 <param name="inputFormat" value="vcf"/>
 <param name="outputFormat" value="vcf"/>
 </output>
 </test>
 -->
 </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>

Mercurial > repos > iuc > snpeff

comparison snpEff.xml @ 3:b24873564cf6 draft