changeset 2:9109c2c3be1e draft

Uploaded

--- a/tool_dependencies.xml	Wed Jul 17 15:05:43 2013 -0400
+++ b/tool_dependencies.xml	Fri Jul 19 09:37:45 2013 -0400
@@ -20,23 +20,6 @@
         <readme>
         </readme>
     </package>
-    <package name="fastqc" version="0.10.1">
-        <install version="1.0">
-            <actions>
-                <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>../FastQC/</source_directory>
-                    <destination_directory>$INSTALL_DIR/FastQC</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/FastQC</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        FastQC needs a java Runtime Environment.
-        </readme>
-    </package>
 </tool_dependency>
 
 

--- a/trim_galore_wrapper.xml	Wed Jul 17 15:05:43 2013 -0400
+++ b/trim_galore_wrapper.xml	Fri Jul 19 09:37:45 2013 -0400
@@ -4,7 +4,6 @@
     <version_command interpreter="perl">trim_galore --version</version_command>
     <requirements>
         <requirement type="package" version="1.1">cutadapt</requirement>
-        <requirement type="package" version="0.10.1">fastqc</requirement>
     </requirements>
     <command interpreter="perl">
         #from glob import glob
@@ -49,7 +48,6 @@
 
         #if $params.settingsType == "custom":
 
-            $params.fastqc
             ## default 20
             --quality $params.quality
             ## default 'AGATCGGAAGAGC'
@@ -178,7 +176,7 @@
         #end if
 
         ## delete the temp_dir
-        ##rm -rf $temp_dir
+        rm -rf $temp_dir
 
     </command>
     <inputs>
@@ -211,7 +209,6 @@
             <when value="default" />
             <!-- Full/advanced params. -->
             <when value="custom">
-                <param name="fastqc" type="boolean" truevalue="--fastqc" falsevalue="" checked="False" label="Run FastQC in the default mode on the FastQ file once trimming is complete" help="" />
                 <param name="quality" type="integer" value="20" label="Trim low-quality ends from reads in addition to adapter removal." help="For more information please see below." />
                 <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed">
                     <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
@@ -330,8 +327,7 @@
 **What it does**
 
 TrimGalore!_ is a wrapper script that makes use of the publically available 
-adapter trimming tool Cutadapt and FastQC for optional quality control once 
-the trimming process has completed.
+adapter trimming tool Cutadapt.
 
 
 .. _TrimGalore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/