Mercurial > repos > bernhardlutz > twistdna

changeset 9:8e7a81fb85be draft

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Uploaded
author bernhardlutz
date Sat, 28 Dec 2013 15:44:55 -0500
parents f339a3ead144
children 771d4a1ec961
files create_input_dat.py create_zip.py standardconfig tool_dependencies.xml twistdna.xml
diffstat 5 files changed, 58 insertions(+), 22 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_input_dat.py	Sat Dec 28 15:44:55 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()
+
--- a/create_zip.py	Tue Dec 24 06:24:59 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import sys
-import zipfile
-
-
-os.chdir(sys.argv[2])
-
-# create zip file in current directory named first argument in folder second argument
-
-zf = zipfile.ZipFile(sys.argv[1], mode='w')
-for files in os.listdir(sys.argv[2]):
-        zf.write(files)
-zf.close()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/standardconfig	Sat Dec 28 15:44:55 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)
+
--- a/tool_dependencies.xml	Tue Dec 24 06:24:59 2013 -0500
+++ b/tool_dependencies.xml	Sat Dec 28 15:44:55 2013 -0500
@@ -4,8 +4,12 @@
             <actions>
                 <action type="make_directory">$INSTALL_DIR/bin</action>
                 <action type="move_file">
-                    <source>create_zip.py</source>
-                    <destination>$INSTALL_DIR/bin</destination>
+                    <source>create_input_dat.py</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="move_file">
+                    <source>standardconfig</source>
+                    <destination>$INSTALL_DIR/</destination>
                 </action>
                 <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>
@@ -17,6 +21,9 @@
                 <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                 </action>
+                <action type="set_environment">
+                    <environment_variable name="TWISTDNA_SCRIPT_PATH" action="set">$INSTALL_DIR</environment_variable>
+                </action>
             </actions>
         </install>
         <readme>Compiling TwistDNA requires a C compiler and gfortran (typically gcc)</readme>
--- a/twistdna.xml	Tue Dec 24 06:24:59 2013 -0500
+++ b/twistdna.xml	Sat Dec 28 15:44:55 2013 -0500
@@ -1,11 +1,15 @@
 <tool id="twistdna" name="TwistDNA" version="0.1.0">
-    <description>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. </description>
+    <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>
-TwistDNA &lt; $input &gt; $outfile
-python create_zip.py $outfile "."
+    #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
+TwistDNA &lt; $input
     </command>
     <stdio>
         <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
@@ -13,11 +17,26 @@
     </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="outfile" format="zip" />
+        <data name="outfile1" format="bed" />
+        <data name="outfile2" format="bed" />
     </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. 
+    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>