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changeset 7:7adfd0589f49 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
author iuc
date Tue, 18 Apr 2017 09:33:56 -0400
parents 20f0429a4bfe
children ce135864629c
files readme.rst snpEff.xml snpEff_databases.xml snpEff_download.xml snpEff_macros.xml test-data/input.vcf test-data/vcf_homhet.vcf tool_dependencies.xml
diffstat 8 files changed, 171 insertions(+), 266 deletions(-) [+]
line wrap: on
line diff
--- a/readme.rst	Mon Dec 19 11:56:53 2016 -0500
+++ b/readme.rst	Tue Apr 18 09:33:56 2017 -0400
@@ -6,14 +6,6 @@
 
 .. _SnpEff: http://snpeff.sourceforge.net/
 
-
-This repository let you automatically install SnpEff and SnpSift.
-This will use the default location for genome reference downloads from the ``snpEff.config`` file:
-
-  data_dir = ~/snpEff/data/
-
-You can manually edit the installed ``snpEff.config`` file and change the location, or you can create a symbolic link to the desired data location from ``~/snpEff``.
-
 The genome reference options used by the tools "SnpEff" (snpEff.xml) and "SnpEff Download" (snpEff_download.xml) are taken from the ``tool-data/snpeffect_genomedb.loc`` file.
 You can fill this file by running the following command:
 
@@ -35,4 +27,3 @@
 .. _Cingolani2012using: http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00035/
 
 Wrapper authors: Jim Johnson
-
--- a/snpEff.xml	Mon Dec 19 11:56:53 2016 -0500
+++ b/snpEff.xml	Tue Apr 18 09:33:56 2017 -0400
@@ -6,23 +6,20 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />
-    <command>
-<![CDATA[
-        @CONDA_SNPEFF_JAR_PATH@ &&
-        java -Xmx6G -jar "\$SNPEFF_JAR_PATH/snpEff.jar" eff
-        -c "\$SNPEFF_JAR_PATH/snpEff.config"
+    <command><![CDATA[
+        snpEff -Xmx8g eff
         -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) != '':
+          #if str($spliceRegion.spliceRegionExonSize)
             -spliceRegionExonSize $spliceRegion.spliceRegionExonSize
           #end if
-          #if $spliceRegion.spliceRegionIntronMin and str($spliceRegion.spliceRegionIntronMin) != '':
+          #if str($spliceRegion.spliceRegionIntronMin)
             -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin
           #end if
-          #if $spliceRegion.spliceRegionIntronMax and str($spliceRegion.spliceRegionIntronMax) != '':
+          #if str($spliceRegion.spliceRegionIntronMax)
             -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax
           #end if
         #end if
@@ -39,63 +36,63 @@
             -no $eff
           #end for
         #end if
-        #if str( $transcripts ) != 'None':
-          -onlyTr $transcripts
+        #if $transcripts
+          -onlyTr '$transcripts'
         #end if
-        #if str( $intervals ) != 'None':     ### fix this for multiple dataset input
-          -interval $intervals
+        #if $intervals     ### fix this for multiple dataset input
+          -interval '$intervals'
         #end if
         #if $statsFile:
-          -stats $statsFile
+          -stats '$statsFile'
         #end if
         #if str($offset) != 'default':
           ${offset}
         #end if
         #if str($chr).strip() != '':
-          -chr "$chr"
+          -chr '$chr'
         #end if
           $noLog
+        ## Regulation names can include parentheses: H3K4me3-MSC_(VB)_enriched_sites
+        ## Enclose them in in single and double quotes, as the conda snpEff bash script will remove outer quotes
         #if $snpDb.genomeSrc == 'cached':
           -dataDir ${snpDb.genomeVersion.fields.path}
-          #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != '':
-            #echo " "
-            #echo ' '.join(str($snpDb.extra_annotations).split(','))
-          #end if
-          #if $snpDb.regulation and str($snpDb.regulation) != '':
-            -reg #echo ' -reg '.join(str($snpDb.regulation).split(','))#
+          #if $snpDb.reg_section.regulation and str($snpDb.reg_section.regulation) != '':
+            #set $regs = [x for x in str($snpDb.reg_section.regulation).split(',')]
+            #for reg in $regs:
+              -reg '"${reg}"'
+            #end for
           #end if
           $snpDb.genomeVersion
         #elif $snpDb.genomeSrc == 'history':
-          -dataDir ${snpDb.snpeff_db.extra_files_path}
-          #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != '':
-            #set xannotations = [' '] + str($snpDb.extra_annotations).split(',')
-            #echo " "
-            #echo ' -'.join($xannotations)
+          -dataDir '${snpDb.snpeff_db.extra_files_path}'
+          #if $snpDb.reg_section.regulation and str($snpDb.reg_section.regulation) != '':
+            #set $regs = [x for x in str($snpDb.reg_section.regulation).split(',')]
+            #for reg in $regs:
+              -reg '"${reg}"'
+            #end for
           #end if
-          #if $snpDb.regulation and str($snpDb.regulation) != '':
-            -reg #echo ' -reg '.join(str($snpDb.regulation).split(','))#
-          #end if
-          ${snpDb.snpeff_db.metadata.genome_version}
+          '${snpDb.snpeff_db.metadata.genome_version}'
         #else
           -download
-          $snpDb.genome_version
+          '$snpDb.genome_version'
         #end if
-        "$input" > "$snpeff_output";
+        '$input' > '$snpeff_output'
         #if $statsFile:
+            &&
             #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, $genes_file_name)#;
+            mkdir '$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.bak -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' "$snpeff_output"
+          sed -i.bak -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' '$snpeff_output'
         #end if
-]]>
-    </command>
+    ]]></command>
     <inputs>
-        <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
+        <param name="input" type="data" format="vcf,tabular,pileup,bed" label="Sequence changes (SNPs, MNPs, InDels)"/>
 
         <param name="inputFormat" type="select" label="Input format">
             <option value="vcf" selected="true">VCF</option>
@@ -127,45 +124,34 @@
                 <param name="genomeVersion" type="select" label="Genome">
                     <!--GENOME    DESCRIPTION-->
                     <options from_data_table="snpeffv_genomedb">
-                           <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/>
-                           <filter type="unique_value" column="2" />
+                            <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/>
+                            <filter type="unique_value" column="2" />
                     </options>
                 </param>
-                <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="snpeffv_annotations">
-                           <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
-                           <filter type="unique_value" column="3" />
-                       </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>
-                       <options from_data_table="snpeffv_regulationdb">
-                           <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
-                           <filter type="unique_value" column="3" />
-                       </options>
-                </param>
+                <section name="reg_section" expanded="false" title="Regulation options">
+                    <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation" help="These are available for only a few genomes">
+                        <options from_data_table="snpeffv_regulationdb">
+                            <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
+                            <filter type="unique_value" column="3" />
+                        </options>
+                    </param>
+                </section>
             </when>
             <when value="history">
-                <param format="snpeffdb" name="snpeff_db" type="data" label="@SNPEFF_VERSION@ Genome Data">
+                <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
                     <options options_filter_attribute="metadata.snpeff_version" >
                         <filter type="add_value" value="@SNPEFF_VERSION@" />
                     </options>
-                    <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ Genome databases.">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator>
+                    <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator>
                 </param>
-                <!-- From metadata -->
-                <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">
-                    <help>These are available for only a few genomes</help>
-                    <options>
-                        <filter type="data_meta" ref="snpeff_db" key="regulation" />
-                    </options>
-                </param>
+                <section name="reg_section" expanded="false" title="Regulation options">
+                    <!-- From metadata -->
+                    <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation" help="These are available for only a few genomes">
+                        <options>
+                            <filter type="data_meta" ref="snpeff_db" key="regulation" />
+                        </options>
+                    </param>
+                </section>
             </when>
             <when value="named">
                 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
@@ -186,7 +172,7 @@
             <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" help="Default: 2">
+        <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases">
             <option value="1">1 base</option>
             <option value="2" selected="true">2 bases</option>
             <option value="3">3 bases</option>
@@ -212,24 +198,33 @@
         </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="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN')</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="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</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>
+            <option value="-hgvsOld">Old notation style notation: E.g. 'c.G123T' instead of 'c.123G>T' and 'X' instead of '*'</option>
+            <option value="-hgvs1LetterAa">Use one letter Amino acid codes in HGVS notation. E.g. p.R47G instead of p.Arg47Gly</option>
+            <option value="-hgvsTrId">Use transcript ID in HGVS notation. E.g. ENST00000252100:c.914C>G instead of c.914C>G</option>
+            <option value="-noShiftHgvs">Do not shift variants according to HGVS notation (most 3prime end)</option>
+            <option value="-noHgvs">Do not add HGVS annotations</option>
+            <option value="-canon">Only use canonical transcripts</option>
+            <option value="-onlyProtein">Only use protein coding transcripts</option>
+            <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
+            <option value="-noExpandIUB">Disable IUB code expansion in input variants</option>
+            <option value="-oicr">Add OICR tag in VCF file</option>
+            <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option>
+            <option value="-noLof">Do not add LOF and NMD annotations</option>
+            <option value="-noMotif">Disable motif annotations</option>
+            <option value="-noNextProt">Disable NextProt annotations</option>
+            <option value="-noInteraction">Disable interaction annotations</option>
+            <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
+            <!--  onlyReg option results in ifrequent exceptions with version 4.3k
+            <option value="-onlyReg">Only use regulation tracks</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="intervals" type="data" format="bed" optional="true" label="Use custom interval file for annotation"/>
+        <param name="transcripts" type="data" format="tabular" 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>
@@ -287,12 +282,11 @@
                     <option value="UTR_5_PRIME">UTR_5_PRIME  (5_prime_UTR_variant) Variant hits 5'UTR region  MODIFIER</option>
                     <option value="UTR_5_DELETED">UTR_5_DELETED  (5_prime_UTR_truncation + exon_loss_variant) The variant deletes an exon which is in the 5'UTR of the transcript  MODERATE</option>
                     <option value="NEXT_PROT">NEXT_PROT  (sequence_feature + exon_loss_variant) A 'NextProt' based annotation. Details are provided in the 'feature type' sub-field (ANN), or in the effect details (EFF).  MODERATE </option>
-
                 </param>
             </when>
         </conditional>
 
-        <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
+        <param name="offset" type="select" display="radio" label="Chromosomal position">
             <option value="default" 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>
@@ -300,7 +294,7 @@
         <param name="chr" type="text" 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.
+               You can prepend any string you want to the chromosome name
             </help>
             <validator type="regex" message="No whitespace allowed">^\S*$</validator>
         </param>
@@ -308,93 +302,38 @@
         <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server"/>
     </inputs>
     <outputs>
-        <data format="vcf" name="snpeff_output" >
+        <data name="snpeff_output" format="vcf">
             <change_format>
                 <when input="outputConditional.outputFormat" value="bed" format="bed" />
                 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
             </change_format>
         </data>
-        <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats">
+        <data name="statsFile" format="html" label="${tool.name} on ${on_string} - stats">
             <filter>generate_stats == True</filter>
         </data>
     </outputs>
     <tests>
-        <!-- Check that an effect was added in out VCF -->
-        <!-- Check for a HTML header indicating that this was successful -->
-        <!--
-        <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"/>
-        <param name="genomeSrc" value="named"/>
-        <param name="genome_version" value="testCase"/>
-        <param name="udLength" value="0"/>
-        <param name="generate_stats" value="False"/>
-        <param name="filterOut" value="+-no-upstream"/>
-        <output name="snpeff_output">
-            <assert_contents>
-            <has_text text="EFF=" />
-            </assert_contents>
-        </output>
+            <param name="input" ftype="vcf" value="input.vcf"/>
+            <param name="inputFormat" value="vcf"/>
+            <param name="outputFormat" value="vcf"/>
+            <param name="genomeSrc" value="named"/>
+            <param name="genome_version" value="ebola_zaire"/>
+            <param name="udLength" value="0"/>
+            <param name="generate_stats" value="False"/>
+            <output name="snpeff_output">
+                <assert_contents>
+                    <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
+                    <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
+                </assert_contents>
+            </output>
         </test>
-        -->
-
-        <test>
-        <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
-        <param name="inputFormat" value="vcf"/>
-        <param name="outputFormat" value="vcf"/>
-        <param name="genomeSrc" value="named"/>
-        <param name="genome_version" value="testCase"/>
-        <param name="udLength" value="0"/>
-        <!--
-        <param name="filterOut" value=""/>
-        -->
-        <param name="generate_stats" value="False"/>
-        <output name="snpeff_output">
-            <assert_contents>
-            <!-- Check that deleletions were evaluated -->
-            <has_text_matching expression="Y\t59030478\t.*intergenic_region" />
-            <!-- Check that insertion on last line was NOT evaluated -->
-            <has_text_matching expression="Y\t59032947\t.*\tGT" />
-            </assert_contents>
-        </output>
-        </test>
-
-        <!-- Check that NO UPSTREAM  effect was added -->
-        <!-- 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"/>
-        <param name="genomeSrc" value="named"/>
-        <param name="genome_version" value="testCase"/>
-        <param name="udLength" value="0"/>
-        <param name="filterOut" value="+-no-upstream"/>
-        <param name="generate_stats" value="False"/>
-        <output name="snpeff_output">
-            <assert_contents>
-            <not_has_text text="UPSTREAM" />
-            </assert_contents>
-        </output>
-        </test>
-        -->
-
     </tests>
     <help><![CDATA[
-
 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
 
 @EXTERNAL_DOCUMENTATION@
-
 ]]>
     </help>
     <expand macro="citations" />
 </tool>
-
--- a/snpEff_databases.xml	Mon Dec 19 11:56:53 2016 -0500
+++ b/snpEff_databases.xml	Tue Apr 18 09:33:56 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="snpEff_databases" name="SnpEff Available Databases" version="@WRAPPER_VERSION@.0">
+<tool id="snpEff_databases" name="SnpEff available databases" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>snpEff_macros.xml</import>
@@ -6,12 +6,9 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />
-    <command>
-<![CDATA[
-    @CONDA_SNPEFF_JAR_PATH@ &&
-    java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" databases |  grep -v '^---' | sed 's/^Genome/#Genome/' | sed  's/  *//g' > "$snpeff_dbs"
-]]>
-    </command>
+    <command><![CDATA[
+snpEff databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/  *//g' > '$snpeff_dbs'
+    ]]></command>
     <inputs>
     </inputs>
     <outputs>
@@ -27,11 +24,8 @@
         </test>
     </tests>
     <help><![CDATA[
-
 @EXTERNAL_DOCUMENTATION@
-
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
 
--- a/snpEff_download.xml	Mon Dec 19 11:56:53 2016 -0500
+++ b/snpEff_download.xml	Tue Apr 18 09:33:56 2017 -0400
@@ -6,14 +6,11 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />
-    <command>
-<![CDATA[
-    @CONDA_SNPEFF_JAR_PATH@ &&
-    java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" download -c "\$SNPEFF_JAR_PATH/snpEff.config" -dataDir "$snpeff_db.files_path" -v "$genome_version"
-]]>
-    </command>
+    <command><![CDATA[
+snpEff download -dataDir '$snpeff_db.files_path' -v '$genome_version'
+    ]]></command>
     <inputs>
-        <param name="genome_version" type="text" 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. GRCh38.86, GRCh37.75, hg38, or GRCm38.86)">
             <help>@SNPEFF_DATABASE_URL@</help>
             <validator type="regex" message="A genome version name is required">\S+</validator>
         </param>
@@ -32,11 +29,7 @@
         </test>
     </tests>
     <help><![CDATA[
-
 @EXTERNAL_DOCUMENTATION@
-
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
-
--- a/snpEff_macros.xml	Mon Dec 19 11:56:53 2016 -0500
+++ b/snpEff_macros.xml	Tue Apr 18 09:33:56 2017 -0400
@@ -1,7 +1,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="4.1">snpEff</requirement>
+            <requirement type="package" version="4.3k">snpeff</requirement>
         </requirements>
     </xml>
   <xml name="stdio">
@@ -10,22 +10,16 @@
         <exit_code range="1:"  level="fatal" description="Error" />
     </stdio>
   </xml>
-  <token name="@CONDA_SNPEFF_JAR_PATH@">if [ -z "\$SNPEFF_JAR_PATH" ]; then export SNPEFF_JAR_PATH=\$(dirname \$(readlink -e \$(which snpEff))); fi</token>
   <xml name="version_command">
     <version_command><![CDATA[
-    if [ -z "$SNPEFF_JAR_PATH" ]; then
-        export SNPEFF_JAR_PATH=$(dirname $(readlink -e $(which snpEff)));
-    fi && java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version
+snpEff -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="@WRAPPER_VERSION@">4.3k</token>
+  <token name="@SNPEFF_VERSION@">SnpEff4.3</token>
+  <token name="@SNPEFF_DATABASE_URL@">https://sourceforge.net/projects/snpeff/files/databases/v4_3/</token>
   <token name="@EXTERNAL_DOCUMENTATION@">
-
-For details about this tool, please go to:
-	http://snpeff.sourceforge.net/SnpEff_manual.html
-
+For details about this tool, please go to: http://snpeff.sourceforge.net/SnpEff_manual.html
   </token>
   <xml name="citations">
       <citations>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.vcf	Tue Apr 18 09:33:56 2017 -0400
@@ -0,0 +1,60 @@
+##fileformat=VCFv4.1
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##contig=<ID="KJ660346",length=18959>
+##reference=http://www.ncbi.nlm.nih.gov/nuccore/KJ660346.2
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	EBOV_2014_EM095	EBOV_2014_G3676	EBOV_2014_G3680	EBOV_2014_G3686	EBOV_2014_G3687	EBOV_2014_G3683	EBOV_2014_EM096	EBOV_2014_EM098	EBOV_2014_EM104	EBOV_2014_EM106	EBOV_2014_EM112	EBOV_2014_EM113	EBOV_2014_EM124	EBOV_2014_G3677	EBOV_2014_G3682	EBOV_2014_G3707	EBOV_2014_G3713	EBOV_2014_G3724	EBOV_2014_G3734	EBOV_2014_G3735	EBOV_2014_G3750	EBOV_2014_G3758	EBOV_2014_G3764	EBOV_2014_G3769	EBOV_2014_G3782	EBOV_2014_G3786	EBOV_2014_G3788	EBOV_2014_G3796	EBOV_2014_G3798	EBOV_2014_G3799	EBOV_2014_G3800	EBOV_2014_G3805	EBOV_2014_G3807	EBOV_2014_G3810	EBOV_2014_G3820	EBOV_2014_G3838	EBOV_2014_G3840	EBOV_2014_G3841	EBOV_2014_G3848	EBOV_2014_NM042	EBOV_2014_G3850	EBOV_2014_EM110	EBOV_2014_EM111	EBOV_2014_EM119	EBOV_2014_G3729	EBOV_2014_G3765	EBOV_2014_G3770	EBOV_2014_G3789	EBOV_2014_G3825	EBOV_2014_G3845	EBOV_2014_G3851	EBOV_2014_G3857	EBOV_2014_EM115	EBOV_2014_EM120	EBOV_2014_G3752	EBOV_2014_G3795	EBOV_2014_G3808	EBOV_2014_G3823	EBOV_2014_EM121	EBOV_2014_G3771	EBOV_2014_G3816	EBOV_2014_G3829	EBOV_2014_G3846	EBOV_2014_G3856	EBOV_2014_G3826	EBOV_2014_G3827	EBOV_2014_G3809	EBOV_2014_G3814	EBOV_2014_G3821	EBOV_2014_G3822	EBOV_2014_G3679	EBOV_2014_G3819	EBOV_2014_G3817	EBOV_2014_G3834	EBOV_2014_G3818	EBOV_2014_G3787	EBOV_2014_G3831	EBOV_2014_G3670	EBOV_2014_KJ660346	EBOV_2014_KJ660347	EBOV_2014_KJ660348
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+KJ660346	15599	.	G	A	.	.	.	GT	1	1	1	0	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
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+KJ660346	18895	.	C	T	.	.	.	GT	0	0	0	0	0	0	0	.	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	0	0	0	0	0	0	0	0	.	0	0	0	0	.	0	.	0	0	0	.	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	0	0	0	0	0	0	0	0	0	0	0	1	1	1
--- a/test-data/vcf_homhet.vcf	Mon Dec 19 11:56:53 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,60 +0,0 @@
-##fileformat=VCFv4.0
-##samtoolsVersion=0.1.15 (r949:203)
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
-##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
-##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
-##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
-##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the site allele frequency of the first ALT allele">
-##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
-##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
-##INFO=<ID=CI95,Number=2,Type=Float,Description="Equal-tail Bayesian credible interval of the site allele frequency at the 95% level">
-##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
-##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
-##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
-##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
-##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
-##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
-##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
-##FORMAT=<ID=PL,Number=.,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">
-##source_20110319.1=/wsu/home/eq/eq83/eq8302/tools/vcftools/bin//vcf-merge s_1_ACAGTGA.vcf.gz s_1_CAGATCA.vcf.gz s_1_CGATGTA.vcf.gz s_1_CTTGTAA.vcf.gz s_1_GCCAATA.vcf.gz s_1_TGACCAA.vcf.gz
-##sourceFiles_20110319.1=0:s_1_ACAGTGA.vcf.gz,1:s_1_CAGATCA.vcf.gz,2:s_1_CGATGTA.vcf.gz,3:s_1_CTTGTAA.vcf.gz,4:s_1_GCCAATA.vcf.gz,5:s_1_TGACCAA.vcf.gz
-##INFO=<ID=SF,Number=.,Type=String,Description="Source File (index to sourceFiles, f when filtered)">
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	s_1_ACAGTGA_sort.bam	s_1_CAGATCA_sort.bam	s_1_CGATGTA_sort.bam	s_1_CTTGTAA_sort.bam	s_1_GCCAATA_sort.bam	s_1_TGACCAA_sort.bam
-Y	3718196	.	C	T	7.59	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-33;G3=4.617e-16,8.575e-07,1;MQ=39;SF=1	GT:GQ:PL	.	1/1:61:38,6,0	.	.	.	.
-Y	3720217	.	A	G	8.65	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,1;DP=2;FQ=-30;G3=4.415e-15,5.291e-06,1;MQ=38;SF=5	GT:GQ:PL	.	.	.	.	.	1/1:53:38,3,0
-Y	3720581	.	A	G	7.80	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,1,0;DP=1;FQ=-30;G3=5.56e-15,5.291e-06,1;MQ=44;SF=1	GT:GQ:PL	.	1/1:53:37,3,0	.	.	.	.
-Y	3721154	.	A	G	13.90	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-33;G3=9.194e-17,8.566e-07,1;MQ=37;SF=3	GT:GQ:PL	.	.	.	1/1:61:45,6,0	.	.
-Y	3721230	.	C	G	21.80	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-33;G3=1.456e-17,8.564e-07,1;MQ=29;SF=3	GT:GQ:PL	.	.	.	1/1:61:53,6,0	.	.
-Y	3744605	.	C	A	3.98	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-33;G3=1.468e-15,8.599e-07,1;MQ=19;SF=2	GT:GQ:PL	.	.	1/1:61:33,6,0	.	.	.
-Y	4433091	.	T	C	11.10	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-33;G3=1.835e-16,8.568e-07,1;MQ=23;SF=5	GT:GQ:PL	.	.	.	.	.	1/1:61:42,6,0
-Y	9945223	.	ATTT	ATTTT	19.80	.	AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=2.906e-18,8.564e-07,1;INDEL;MQ=45;SF=0,2	GT:GQ:PL	1/1:61:60,6,0	.	1/1:61:57,6,0	.	.	.
-Y	9987395	.	TTAT	TT	80.40	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,1,2;DP=3;FQ=-43.5;G3=5.464e-26,5.886e-08,1;INDEL;MQ=43;SF=5	GT:GQ:PL	.	.	.	.	.	1/1:72:120,9,0
-Y	10011604	.	C	CTT	119.17	.	AC=12;AF1=1;AN=12;CI95=1,1;DP4=0,0,7,0;DP=9;FQ=-55.5;G3=4.948e-32,3.15e-11,1;INDEL;MQ=33;SF=0,1,2,3,4,5	GT:GQ:PL	1/1:99:139,21,0	1/1:96:134,24,0	1/1:99:168,36,0	1/1:99:159,45,0	1/1:99:185,33,0	1/1:99:175,39,0
-Y	10011748	.	GAAAAAA	GAAAAAAA	23.70	.	AC=6;AF1=0.5;AN=12;CI95=0.5,0.5;DP4=12,12,11,10;DP=51;FQ=33.5;G3=1.256e-14,1,1.991e-19;INDEL;MQ=33;PV4=1,0.49,0.012,0.2;SF=0,1,2,3,4,5	GT:GQ:PL	0/0:71:68,0,92	1/1:55:52,0,77	1/1:71:69,0,75	1/1:69:66,0,79	1/1:56:53,0,80	1/1:62:59,0,98
-Y	10011894	.	ATTATTTATTT	ATTATTT	58.62	.	AC=4;AF1=0.5;AN=8;CI95=0.5,0.5;DP4=4,11,0,6;DP=34;FQ=32.5;G3=1.991e-14,1,7.924e-52;INDEL;MQ=35;PV4=0.28,0.049,0.14,0.2;SF=1,3,4,5	GT:GQ:PL	.	0/0:70:67,0,254	.	1/1:99:152,0,255	1/1:83:80,0,255	1/1:89:86,0,255
-Y	10011930	.	ACT	A	90.85	.	AC=2;AF1=0.5;AN=4;CI95=0.5,0.5;DP4=2,6,1,3;DP=17;FQ=16.6;G3=3.155e-11,1,1.991e-34;INDEL;MQ=35;PV4=1,0.00044,0.33,1;SF=0,5	GT:GQ:PL	0/0:54:51,0,167	.	.	.	.	0/0:99:206,0,255
-Y	10011935	.	C	CT	83.83	.	AC=3;AF1=0.5;AN=6;CI95=0.5,0.5;DP4=1,8,2,5;DP=23;FQ=90.3;G3=1.256e-28,1,5e-26;INDEL;MQ=39;PV4=0.55,1,0.15,1;SF=1,2,4	GT:GQ:PL	.	0/0:99:138,0,125	1/1:92:89,0,148	.	1/1:99:138,0,171	.
-Y	10011966	.	ATT	AT	79.38	.	AC=6;AF1=0.5;AN=12;CI95=0.5,0.5;DP4=1,6,0,2;DP=14;FQ=5.09;G3=1.991e-12,1,1.256e-28;INDEL;MQ=38;PV4=1,1,0.46,0.088;SF=0,1,2,3,4,5	GT:GQ:PL	1/1:41:38,0,92	1/1:76:73,0,109	1/1:99:181,0,109	1/1:99:114,0,103	1/1:99:139,0,171	1/1:99:155,0,144
-Y	10028061	.	CA	CAA	28.40	.	AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,2,1;DP=9;FQ=-43.5;G3=2.739e-22,5.886e-08,1;INDEL;MQ=37;SF=4,5	GT:GQ:PL	.	.	.	.	1/1:72:83,9,0	0/0:61:52,6,0
-Y	10029194	.	CA	C	73.47	.	AC=10;AF1=0.7304;AN=12;CI95=0.5,1;DP4=2,0,7,3;DP=19;FQ=-32.5;G3=2.922e-150,0.9991,0.000854;INDEL;MQ=25;PV4=1,0.4,1,0.23;SF=0,1,2,3,4,5	GT:GQ:PL	0/0:3:93,0,2	1/1:85:100,17,0	1/1:99:181,36,0	1/1:90:107,18,0	1/1:3:104,0,2	1/1:70:90,10,0
-Y	10029452	.	CAA	CAAA	7.26	.	AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,4,0;DP=13;FQ=-46.5;G3=2.341e-18,6.106e-08,1;INDEL;MQ=26;SF=3,4	GT:GQ:PL	.	.	.	1/1:72:50,12,0	1/1:72:42,12,0	.
-Y	10037877	.	GCCC	GCCCC	14.40	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=3;FQ=-40.5;G3=1.456e-17,8.564e-07,1;INDEL;MQ=29;SF=2	GT:GQ:PL	.	.	1/1:61:53,6,0	.	.	.
-Y	13266272	.	TTTT	TTTTATTT	51.50	.	AC=1;AF1=0.5;AN=2;CI95=0.5,0.5;DP4=5,1,7,0;DP=15;FQ=54.5;G3=7.924e-19,1,3.155e-24;INDEL;MQ=30;PV4=0.46,1,0.078,0.00035;SF=3	GT:GQ:PL	.	.	.	0/0:92:89,0,116	.	.
-Y	13268110	.	GC	GCC	3.66	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-40.5;G3=2.911e-16,8.571e-07,1;INDEL;MQ=23;SF=2	GT:GQ:PL	.	.	1/1:61:40,6,0	.	.	.
-Y	13292082	.	TCCCCCCCCCC	TCCCCCCC	14.40	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=1.456e-17,8.564e-07,1;INDEL;MQ=29;SF=3	GT:GQ:PL	.	.	.	1/1:61:53,6,0	.	.
-Y	13297070	.	AGGTGGTGGTGGT	AGGTGGTGGT	12.70	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,1;DP=1;FQ=-37.5;G3=2.782e-16,5.287e-06,1;INDEL;MQ=50;SF=5	GT:GQ:PL	.	.	.	.	.	1/1:53:50,3,0
-Y	13312198	.	CGGGGG	CGGGG	14.87	.	AC=5;AF1=1;AN=6;CI95=0.5,1;DP4=2,0,10,0;DP=12;FQ=-43.5;G3=1.373e-19,5.886e-08,1;INDEL;MQ=24;PV4=1,0.44,1,0.019;SF=1,4,5	GT:GQ:PL	.	1/1:72:56,9,0	.	.	1/1:70:57,10,0	1/1:44:48,0,42
-Y	13312608	.	CA	CAA	22.50	.	AC=1;AF1=0.5032;AN=2;CI95=0.5,0.5;DP4=2,0,7,0;DP=16;FQ=-15.6;G3=4.937e-25,1,1.272e-08;INDEL;MQ=24;PV4=1,1,0.093,1;SF=2	GT:GQ:PL	.	.	0/0:22:60,0,19	.	.	.
-Y	13402810	.	TAGAGA	TAGA	29.80	.	AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,1,1;DP=2;FQ=-40.5;G3=7.299e-19,8.564e-07,1;INDEL;MQ=33;SF=0,2	GT:GQ:PL	1/1:61:66,6,0	.	1/1:72:72,9,0	.	.	.
-Y	21153016	.	AG	ATG	213.83	.	AC=12;AF1=1;AN=12;CI95=1,1;DP4=0,0,6,9;DP=15;FQ=-79.5;G3=7.905e-54,1e-18,1;INDEL;MQ=43;SF=0,1,2,3,4,5	GT:GQ:PL	1/1:99:255,45,0	1/1:99:.,.,0	1/1:99:255,87,0	1/1:99:.,.,0	1/1:99:255,78,0	1/1:99:.,.,0
-Y	21153067	.	CCA	C	46.50	.	AC=1;AF1=0.5;AN=2;CI95=0.5,0.5;DP4=8,4,5,0;DP=18;FQ=49.5;G3=7.924e-18,1,5e-52;INDEL;MQ=39;PV4=0.26,0.08,0.035,1;SF=3	GT:GQ:PL	.	.	.	0/0:87:84,0,255	.	.
-Y	26325233	.	TGAGAGAGAGAGA	TGAGAGAGAGA	22.20	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-40.5;G3=2.308e-18,8.564e-07,1;INDEL;MQ=33;SF=0	GT:GQ:PL	1/1:61:61,6,0	.	.	.	.	.
-Y	28588049	.	ACATCAT	ACAT	7.35	.	AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,1,0;DP=1;FQ=-37.5;G3=1.108e-15,5.288e-06,1;INDEL;MQ=44;SF=1,3	GT:GQ:PL	.	1/1:53:44,3,0	.	1/1:53:44,3,0	.	.
-Y	59030478	.	AAAACAAACAAACAAACAAACAAACAAA	AAAACAAACAAACAAA	14.40	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=1.456e-17,8.564e-07,1;INDEL;MQ=29;SF=2	GT:GQ:PL	.	.	1/1:61:53,6,0	.	.	.
-Y	59032947	.	GTT	GTTT	28.20	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=5.798e-19,8.564e-07,1;INDEL;MQ=37;SF=5	GT:GQ:PL	.	.	.	.	.	1/1:61:67,6,0
--- a/tool_dependencies.xml	Mon Dec 19 11:56:53 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <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>