# HG changeset patch
# User iuc
# Date 1465308197 14400
# Node ID b24873564cf6ab4dbb2e2f5468a2d422107d0371
# Parent  e09ce114d2406d9cee9723f2976242d577ece94f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31

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
@@ -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>
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
@@ -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>
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
@@ -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>
 
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
@@ -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>
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
@@ -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:
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
@@ -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>
-