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changeset 5:92b80578fa22 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a
author iuc
date Mon, 04 May 2015 22:37:25 -0400
parents b86c907031ad
children 9ec1cb6f760d
files snpEff.xml snpEff_databases.xml snpEff_download.xml
diffstat 3 files changed, 19 insertions(+), 19 deletions(-) [+]
line wrap: on
line diff
--- a/snpEff.xml	Wed Apr 29 11:56:04 2015 -0400
+++ b/snpEff.xml	Mon May 04 22:37:25 2015 -0400
@@ -1,22 +1,23 @@
 <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" />
     <command>
 <![CDATA[
-        java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff 
-        -c \$SNPEFF_JAR_PATH/snpEff.config 
+        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 $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__ != '':
           #echo " "
@@ -33,15 +34,15 @@
           -interval $intervals
         #end if
         #if $statsFile:
-          -stats $statsFile 
+          -stats $statsFile
         #end if
         #if $offset.__str__ != 'default':
-          ${offset} 
+          ${offset}
         #end if
         #if $chr.__str__.strip() != '':
-          -chr "$chr" 
+          -chr "$chr"
         #end if
-          $noLog 
+          $noLog
         #if $snpDb.genomeSrc == 'cached':
           -dataDir ${snpDb.genomeVersion.fields.path}
           #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
@@ -63,7 +64,7 @@
             -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
           #end if
           ${snpDb.snpeff_db.metadata.genome_version}
-        #else 
+        #else
           -download
           $snpDb.genome_version
         #end if
@@ -252,7 +253,6 @@
             <filter>generate_stats == True</filter>
         </data>
     </outputs>
-    <expand macro="stdio" />
     <tests>
         <!-- Check that an effect was added in out VCF -->
         <!-- Check for a HTML header indicating that this was successful -->
@@ -262,7 +262,7 @@
             <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"/>
@@ -281,7 +281,7 @@
             </assert_contents>
         </output>
         </test>
-        --> 
+        -->
 
         <test>
         <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
--- a/snpEff_databases.xml	Wed Apr 29 11:56:04 2015 -0400
+++ b/snpEff_databases.xml	Mon May 04 22:37:25 2015 -0400
@@ -1,12 +1,13 @@
 <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" />
     <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' > $snpeff_dbs
 ]]>
     </command>
     <inputs>
@@ -14,7 +15,6 @@
     <outputs>
         <data format="tabular" name="snpeff_dbs" label="${tool.name} @SNPEFF_VERSION@ available databases" />
     </outputs>
-    <expand macro="stdio" />
     <help>
 
 @EXTERNAL_DOCUMENTATION@
--- a/snpEff_download.xml	Wed Apr 29 11:56:04 2015 -0400
+++ b/snpEff_download.xml	Mon May 04 22:37:25 2015 -0400
@@ -1,12 +1,13 @@
 <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" />
     <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 $genome_version
 ]]>
     </command>
     <inputs>
@@ -18,7 +19,6 @@
     <outputs>
         <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" />
     </outputs>
-    <expand macro="stdio" />
     <help>
 
 @EXTERNAL_DOCUMENTATION@