Mercurial > repos > bernhardlutz > twistdna

changeset 2:43e514ee6a1e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Deleted selected files
author bernhardlutz
date Mon, 23 Dec 2013 17:05:24 -0500
parents 919021a7806d
children 69d82e5f69bb
files tool_dependencies.xml twistdna.xml
diffstat 2 files changed, 0 insertions(+), 37 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Mon Dec 23 16:38:25 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<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">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>
--- a/twistdna.xml	Mon Dec 23 16:38:25 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-<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>