Mercurial > repos > iuc > snpsift_genesets

diff snpSift_macros.xml @ 3:847db7b39bdc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author iuc
date Mon, 05 Dec 2016 12:06:09 -0500
parents 9ba6e2c298ab
children d12a810c837e
line wrap: on
line diff
--- a/snpSift_macros.xml	Mon Sep 19 14:43:55 2016 -0400
+++ b/snpSift_macros.xml	Mon Dec 05 12:06:09 2016 -0500
@@ -1,7 +1,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="4.1">snpEff</requirement>
+            <requirement type="package" version="4.1">snpsift</requirement>
         </requirements>
     </xml>
   <xml name="stdio">
@@ -10,12 +10,11 @@
         <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>
+  <token name="@CONDA_SNPSIFT_JAR_PATH@">if [ -z "\$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=\$(dirname \$(readlink -e \$(which SnpSift))); 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
+    if [ -z "$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=$(dirname $(readlink -e $(which SnpSift))); fi &&
+    java -jar "$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp 2>&1|head -n 1
     ]]></version_command>
   </xml>
   <token name="@WRAPPER_VERSION@">4.1</token>
@@ -25,16 +24,6 @@
 	http://snpeff.sourceforge.net/SnpEff_manual.html
 
   </token>
-  <token name="@CITATION_SECTION@">------
-
-**Citation**
-
-For the underlying tool, please cite the following two publications:
-
-SnpSift citation:
-"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3:35, 2012.
-
-  </token>
   <xml name="citations">
       <citations>
         <citation type="doi">10.3389/fgene.2012.00035</citation>