changeset 9:c13fa2748191 draft

Uploaded

--- a/FastQC/rgFastQC.xml	Mon Jun 03 23:11:58 2013 -0400
+++ b/FastQC/rgFastQC.xml	Mon Jun 03 23:25:42 2013 -0400
@@ -1,13 +1,13 @@
 <tool name="FastQC: Comprehensive QC" id="fastqc" version="0.53">
   <description>reporting for short read sequence</description>
   <command interpreter="python">
-    rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" -e "\$FASTQC_INSTALL_PATH/fastqc"
+    rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" -e "\$FASTQC_BINARY_PATH"
 #if $contaminants.dataset and str($contaminants) > ''
 -c "$contaminants"
 #end if
   </command>
   <requirements>
-    <requirement type="set_environment">FASTQC_INSTALL_PATH</requirement>
+    <requirement type="set_environment">FASTQC_BINARY_PATH</requirement>
     <requirement type="package" version="0.10.1">FastQC</requirement>
   </requirements>
   <inputs>

--- a/FastQC/tool_dependencies.xml	Mon Jun 03 23:11:58 2013 -0400
+++ b/FastQC/tool_dependencies.xml	Mon Jun 03 23:25:42 2013 -0400
@@ -1,11 +1,11 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <set_environment version="1.0">
-        <environment_variable name="FASTQC_INSTALL_PATH" action="set_to">$INSTALL_DIR/FastQC</environment_variable>   
-    </set_environment>
     <package name="FastQC" version="0.10.1">
         <install version="1.0">
             <actions>
+                <action type="set_environment">
+                    <environment_variable name="FASTQC_BINARY_PATH">$INSTALL_DIR/FastQC/fastqc</environment_variable>
+                </action>
                 <action type="download_by_url">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip</action>
                 <action type="move_directory_files">
                     <source_directory>./</source_directory>