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diff snpEff.xml @ 2:6ad9205c1307

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Update to SnpEff version 3.3
author Jim Johnson <jj@umn.edu>
date Fri, 04 Oct 2013 09:09:29 -0500
parents e1d9f6a0ad53
children 8952990fcab9
line wrap: on
line diff
--- a/snpEff.xml	Thu Jul 04 09:49:15 2013 -0500
+++ b/snpEff.xml	Fri Oct 04 09:09:29 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="snpEff" name="SnpEff" version="3.2">
+<tool id="snpEff" name="SnpEff" version="3.3">
 	<description>Variant effect and annotation</description>
 	<!-- 
 	    You will need to change the path to wherever your installation is.
@@ -61,30 +61,34 @@
 
 	-->
 	<requirements>
-		<requirement type="package" version="3.2">snpEff</requirement>
+		<requirement type="package" version="3.3">snpEff</requirement>
 	</requirements>
 	<command>
-SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
+SNPEFF_DATA_DIR=`grep '^data_dir' \$SNPEFF_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
 eval "if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ;
-then java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar download  -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion ;
+then java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar download  -c \$SNPEFF_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 
+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 
+  $filterIn 
 #end if
 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter':
-  -$filterHomHet 
+  $filterHomHet 
 #end if
 #if $annotations and $annotations.__str__ != '':
-  -#slurp
-  #echo ' -'.join($annotations.__str__.split(','))
+  #echo ' '.join($annotations.__str__.split(','))
+#end if
+#if $extra_annotations and $extra_annotations.__str__ != '':
+  #echo ' '.join($extra_annotations.__str__.split(','))
+#end if
+#if $regulation and $regulation.__str__ != '':
+  -reg #echo ' -reg '.join($regulation.__str__.split(','))#
 #end if
 #if $filterOut and $filterOut.__str__ != '':
-  -#slurp
-  #echo ' -'.join($filterOut.__str__.split(','))
+  #echo ' '.join($filterOut.__str__.split(','))
 #end if
 #if str( $transcripts ) != 'None':
   -onlyTr $transcripts
@@ -96,7 +100,7 @@
   -stats $statsFile 
 #end if
 #if $offset.__str__ != '':
-  -${offset} 
+  ${offset} 
 #end if
 #if $chr.__str__.strip() != '':
   -chr "$chr" 
@@ -150,35 +154,43 @@
 
         	<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). 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). 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>
+        	</param>
+
+        	<param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations">
+                       <help>These are available for only a few genomes</help>
+                       <!--GENOME	REG_NAME  -->
+                       <options from_data_table="snpeff_annotations">
+                               <filter type="param_value" ref="genomeVersion" key="genome" column="0" />
+                       </options>
         	</param>
 
         	<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>
                        <!--GENOME	REG_NAME  -->
-                       <options from_data_table="snpeffect_regulationdb">
-				<filter type="param_value" ref="genomeVersion" key="name" column="1" />
+                       <options from_data_table="snpeff_regulationdb">
+                               <filter type="param_value" ref="genomeVersion" key="genome" column="0" />
                        </options>
         	</param>
 
@@ -186,21 +198,21 @@
         	<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="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">
 			<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>
+			<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="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.">
                                        <validator type="regex" message="No whitespace allows">^\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"/>
@@ -233,9 +245,7 @@
                 <param name="filterHomHet" value="no_filter"/>
                 <param name="filterIn" value="no_filter"/>
                 <param name="generate_stats" value="False"/>
-                <!--
-                <param name="filterOut" value="no-upstream"/>
-                -->
+                <param name="filterOut" value="+-no-upstream"/>
                 <output name="snpeff_output">
                     <assert_contents>
                         <!-- Check that an effect was added -->
@@ -258,7 +268,7 @@
                 <param name="outputFormat" value="vcf"/>
                 <param name="genomeVersion" value="testCase"/>
                 <param name="udLength" value="0"/>
-                <param name="filterHomHet" value="het"/>
+                <param name="filterHomHet" value="+-het"/>
                 <param name="filterIn" value="no_filter"/>
                 <!--
                 <param name="filterOut" value=""/>
@@ -300,7 +310,7 @@
                 <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="filterOut" value="+-no-upstream"/>
                 <param name="generate_stats" value="False"/>
                 <output name="snpeff_output">
                     <assert_contents>