changeset 0:963fc31e3269 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Oct 09 09:17:29 2015 -0400
@@ -0,0 +1,21 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="wigmaker" version="3">
+        <install version="1.0">
+            <actions>
+                <action type="shell_command">git clone git://git.code.sf.net/p/wigmaker/code wigmaker</action>
+                <action type="make_directory">$INSTALL_DIR/jars</action>
+                <action type="move_file">
+                    <source>WigMaker3.jar</source>
+                    <destination>$INSTALL_DIR/jars</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme></readme>
+    </package>
+</tool_dependency>
+
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wigmaker.sh	Fri Oct 09 09:17:29 2015 -0400
@@ -0,0 +1,21 @@
+#! /bin/bash
+
+input=$1
+output=$2
+wigmaker=$3
+
+inputfile=`basename $input`
+dir=`dirname $input`
+
+cd $dir
+rm $dir/wigs_for_*.wig.gz > /dev/null 2>&1
+rm $dir/wigs_for_*.wig > /dev/null 2>&1
+
+prefix=`echo $input | perl -ne '(\$prefix) = \$_ =~ /(dataset_[0-9]+)/; print \$prefix'`
+
+java -Djava.io.tmpdir=/tmp -Xmx2G -jar $wigmaker $inputfile
+
+cp $dir/wigs_for_$prefix.wig $output
+rm $dir/wigs_for_$prefix.wig
+rm $dir/wigs_for_$prefix.wig.gz
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wigmaker.xml	Fri Oct 09 09:17:29 2015 -0400
@@ -0,0 +1,28 @@
+<tool id="wigmaker" name="WigMaker" version="3">
+  <description>for BED files</description>
+
+  <requirements>
+    <requirement type="package" version="3">wigmaker</requirement>
+  </requirements>
+
+  <command interpreter="bash">wigmaker.sh $input $output \$JAVA_JAR_PATH/WigMaker3.jar</command>
+  <inputs>
+    <param format="interval" name="input" type="data" label="Source file"/>
+  </inputs>
+  <outputs>
+    <data format="wig" name="output" label="${tool.name} on ${on_string} (wig)" />
+  </outputs>
+ 
+  <tests>
+    <test>
+      <param name="input" value="fa_gc_content_input.fa"/>
+      <output name="out_file" file="fa_gc_content_output.txt"/>
+    </test>
+  </tests>
+
+  <help>
+     This tool generates WIG files from BED files. (Developped by Tao Ye).
+  </help>
+</tool>
+
+