changeset 4:698ef30638a8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d

--- a/snpEff.xml	Tue Jun 07 10:03:17 2016 -0400
+++ b/snpEff.xml	Fri Sep 16 13:06:42 2016 -0400
@@ -8,6 +8,7 @@
     <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"
         -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
@@ -359,9 +360,9 @@
         <output name="snpeff_output">
             <assert_contents>
             <!-- Check that deleletions were evaluated -->
-            <has_text_matching expression="Y\t59030478\t.*EFF=INTERGENIC" />
+            <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.*SF=5\tGT" />
+            <has_text_matching expression="Y\t59032947\t.*\tGT" />
             </assert_contents>
         </output>
         </test>

--- a/snpEff_databases.xml	Tue Jun 07 10:03:17 2016 -0400
+++ b/snpEff_databases.xml	Fri Sep 16 13:06:42 2016 -0400
@@ -8,6 +8,7 @@
     <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>

--- a/snpEff_download.xml	Tue Jun 07 10:03:17 2016 -0400
+++ b/snpEff_download.xml	Fri Sep 16 13:06:42 2016 -0400
@@ -8,6 +8,7 @@
     <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>

--- a/snpEff_macros.xml	Tue Jun 07 10:03:17 2016 -0400
+++ b/snpEff_macros.xml	Fri Sep 16 13:06:42 2016 -0400
@@ -10,8 +10,13 @@
         <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>java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version</version_command>
+    <version_command><![CDATA[
+    if [ -z "$SNPEFF_JAR_PATH" ]; then
+        export SNPEFF_JAR_PATH=$(dirname $(readlink -e $(which snpEff)));
+    fi && java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version
+    ]]></version_command>
   </xml>
   <token name="@WRAPPER_VERSION@">4.1</token>
   <token name="@SNPEFF_VERSION@">SnpEff4.1</token>
@@ -22,16 +27,6 @@
 	http://snpeff.sourceforge.net/SnpEff_manual.html
 
   </token>
-  <token name="@CITATION_SECTION@">------
-
-**Citation**
-
-For the underlying tool, please cite the following two publications:
-
-SnpEff citation:
-"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly 6(2):80-92, 2012
-
-  </token>
   <xml name="citations">
       <citations>
         <citation type="doi">10.4161/fly.19695</citation>