changeset 3:69d82e5f69bb draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Dec 23 17:05:31 2013 -0500
@@ -0,0 +1,16 @@
+<tool_dependency>
+    <package name="twistdna" version="1.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://www.cbp.ens-lyon.fr/lib/exe/fetch.php?media=developpement:productions:logiciels:twist-dna_1.1.tar.gz</action>
+                <action type="shell_command">make </action>
+                <action type="shell_command">mkdir $INSTALL_DIR/bin</action>
+                <action type="shell_command">cp TwistDNA $INSTALL_DIR/bin/TwistDNA </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Compiling TwistDNA requires a C compiler and gfortran (typically gcc)</readme>
+    </package>
+</tool_dependency>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/twistdna.xml	Mon Dec 23 17:05:31 2013 -0500
@@ -0,0 +1,22 @@
+<tool id="twistdna" name="TwistDNA" version="0.1.0">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="1.1">twistdna</requirement>
+    </requirements>
+    <command>
+TwistDNA $input $outfile
+    </command>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+    </stdio>
+    <inputs>
+        <param format="fasta" name="input" type="data" label="Input Alignment File" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format="zip" />
+    </outputs>
+    <help>**What it does**
+     Local opening of the DNA double-helix is required in many fundamental biological processes and is in part controlled by the degree of superhelicity imposed in vivo by the protein machinery. In particular, positions of superhelically destabilized regions correlate with regulatory sites along the genome. Based on a self-consistent linearization of a thermodynamic model of superhelical DNA introduced by Benham, we have developed Twist-DNA, a program that predicts the locations of these regions by efficiently computing base-pair and bubble opening probabilities in genomic DNA. The program allows visualization of results in standard genome browsers to compare DNA opening properties to other available datasets. 
+    </help>
+</tool>