Mercurial > repos > bernhardlutz > twistdna

changeset 19:cd586cf1b192 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bernhardlutz
date Sat, 28 Dec 2013 16:46:34 -0500
parents 7b67355ee7ca
children b89c9c78ef29
files create_input_dat.py standardconfig tool_dependencies.xml twistdna.xml
diffstat 4 files changed, 89 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_input_dat.py	Sat Dec 28 16:46:34 2013 -0500
@@ -0,0 +1,17 @@
+#!/usr/bin/env python
+
+import os
+import sys
+
+
+file = "input.dat"
+o = open( file, 'w+' )
+o.write(sys.argv[1]+'\n')
+o.write(sys.argv[2]+'\n')
+o.write(sys.argv[3]+'\n')
+o.write(sys.argv[4]+'\n')
+o.write(sys.argv[5]+'\n')
+o.write(sys.argv[6]+'\n')
+o.write(sys.argv[7]+'\n')
+o.close()
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/standardconfig	Sat Dec 28 16:46:34 2013 -0500
@@ -0,0 +1,8 @@
+37	::Temperature T in Celsius (default 37 C)
+-0.06 	::Superhelical density Sigma (default -0.06)
+0.1	::Salt concentration CNa (default 0.1 M)
+1	::Smallest bubble size bsizemin
+0	::Largest bubble size bsizemax
+1	::Bubble size step bstep
+-3.0	::Bubble storing threshold (default -3)
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sat Dec 28 16:46:34 2013 -0500
@@ -0,0 +1,22 @@
+<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="make_directory">$INSTALL_DIR/bin</action>
+                <action type="move_file">
+                    <source>TwistDNA</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="TWISTDNA_SCRIPT_PATH" action="set_to">$INSTALL_DIR</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	Sat Dec 28 16:46:34 2013 -0500
@@ -0,0 +1,42 @@
+<tool id="twistdna" name="TwistDNA" version="0.1.0">
+    <description>Twist-DNA allows visualization of results in standard genome browsers to compare DNA opening properties to other available datasets</description>
+    <requirements>
+        <requirement type="package" version="1.1">twistdna</requirement>
+    </requirements>
+    <command>
+    #if $advanced == true:
+        python \$TWISTDNA_SCRIPT_PATH/create_input_dat.py $temperature $sigma $salt $small_bubble $large_bubble $bubble_size_step $threshold
+    #else
+        cp \$TWISTDNA_SCRIPT_PATH/standardconfig input.dat
+    #end if
+TwistDNA &lt; $input
+    </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" />
+        <conditional name="check">
+            <param name="advanced" type="boolean" truevalue="yes" falsevalue="no" label="Show advanced Options" help="" checked="false" />
+            <when value="yes">
+                <param name="temperature" label="Temperature in Celsius" type="float" value="37" />
+                <param name="sigma" label="Superhelical density Sigma" type="float" value="-0.06" />
+                <param name="salt" label="Salt concentration CNa" type="float" value="0.1" />
+                <param name="small_bubble" label="Smallest bubble size bsizemin" type="float" value="1" />
+                <param name="large_bubble" label="Largest bubble size bsizemax" type="float" value="0" />
+                <param name="bubble_size_step" label="Bubble size step bstep" type="float" value="1" />
+                <param name="threshold" label="Bubble storing threshold" type="float" value="-3.0" />
+            </when>
+         </conditional>
+    </inputs>
+    <outputs>
+        <data name="outfile1" format="bed" />
+        <data name="outfile2" format="bed" />
+    </outputs>
+    <help>**What it does**
+    http://www.cbp.ens-lyon.fr/doku.php?id=developpement:productions:logiciels:twistdna
+
+    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>