# HG changeset patch
# User davidvanzessen
# Date 1427706405 14400
# Node ID 257e98fd3b54ea24dc018853395da0d846516d32
# Parent  b0242cd1da349bb893c2916f999dda83618bd782
Uploaded

diff -r b0242cd1da34 -r 257e98fd3b54 merge_and_filter.r
diff -r b0242cd1da34 -r 257e98fd3b54 mutation_analysis.r
diff -r b0242cd1da34 -r 257e98fd3b54 mutation_analysis.xml
--- a/mutation_analysis.xml	Thu Mar 26 10:16:20 2015 -0400
+++ b/mutation_analysis.xml	Mon Mar 30 05:06:45 2015 -0400
@@ -10,6 +10,9 @@
 		<data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/>
 	</outputs>
 	<help>
-		there is no help
+		Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis.
 	</help>
+	<requirements>
+    <requirement type="package" version="0.5.9">bwa</requirement>
+	</requirements>
 </tool>
diff -r b0242cd1da34 -r 257e98fd3b54 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Mar 30 05:06:45 2015 -0400
@@ -0,0 +1,24 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<set_environment version="1.0">            
+  </set_environment>
+    
+	<package name="blastn" version="1.0.0"> 
+        <install version="1.0">
+            <actions>
+							<action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-x64-linux.tar.gz</action>
+							<action type="move_file">
+								<source>bin/blastn</source>
+								<destination>$INSTALL_DIR</destination>
+							</action>
+							<action type="set_environment">
+								<environment_variable name="BLASTN" action="set_to">$INSTALL_DIR</environment_variable>
+							</action>
+            </actions>
+        </install>
+        <readme>
+					downloads blast (ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-x64-linux.tar.gz) and keeps the blastn executable
+        </readme>
+    </package>
+</tool_dependency>
+
diff -r b0242cd1da34 -r 257e98fd3b54 wrapper.sh
--- a/wrapper.sh	Thu Mar 26 10:16:20 2015 -0400
+++ b/wrapper.sh	Mon Mar 30 05:06:45 2015 -0400
@@ -15,9 +15,9 @@
 
 
 echo "identification"
-python $dir/gene_identification.py --input $PWD/summary.txt --output $PWD/annotatedsummary.txt
+python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/annotatedsummary.txt
 echo "merging"
-Rscript $dir/merge_and_filter.r $PWD/annotatedsummary.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/merged.txt $outdir/unmatched.txt
+Rscript $dir/merge_and_filter.r $outdir/annotatedsummary.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/merged.txt $outdir/unmatched.txt
 
 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm"
 echo "R mutation analysis"