Mercurial > repos > bernhardlutz > twistdna

changeset 20:b89c9c78ef29 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bernhardlutz
date Thu, 09 Jan 2014 16:05:38 -0500
parents cd586cf1b192
children
files create_input_dat.py standardconfig tool_dependencies.xml twistdna.xml
diffstat 4 files changed, 43 insertions(+), 38 deletions(-) [+]
line wrap: on
line diff
--- a/create_input_dat.py	Sat Dec 28 16:46:34 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-#!/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/standardconfig	Sat Dec 28 16:46:34 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-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	Sat Dec 28 16:46:34 2013 -0500
+++ b/tool_dependencies.xml	Thu Jan 09 16:05:38 2014 -0500
@@ -1,4 +1,7 @@
 <tool_dependency>
+    <set_environment version="1.0">
+        <environment_variable name="TWISTDNA_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
     <package name="twistdna" version="1.1">
         <install version="1.0">
             <actions>
@@ -12,9 +15,6 @@
                 <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$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>
--- a/twistdna.xml	Sat Dec 28 16:46:34 2013 -0500
+++ b/twistdna.xml	Thu Jan 09 16:05:38 2014 -0500
@@ -4,12 +4,16 @@
         <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
+cp $configfile "input.dat";
+mkdir param;
+mkdir outputs;
+cp $enthalpy "param/param_enthalpy.dat";
+cp $entropy "param/param_entropy.dat";
+TwistDNA &lt; $input;
+##remove the first line, because there they are useless
+tail -n+2 outputs/bubblethresh.bed | tr -s ' ' '\t' > $outfile1;
+tail -n+2 outputs/openproba.bed | tr -s ' ' '\t' > $outfile2;
+
     </command>
     <stdio>
         <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
@@ -18,18 +22,44 @@
     <inputs>
         <param format="fasta" name="input" type="data" label="Input Alignment File" />
         <conditional name="check">
-            <param name="advanced" type="boolean" truevalue="yes" falsevalue="no" label="Show advanced Options" help="" checked="false" />
+            <param name="advanced" type="select" label="Show advanced Options" help="" checked="false">
+                <option value="yes">Yes</option>
+                <option value="no">No</option>
+            </param>
             <when value="yes">
                 <param name="temperature" label="Temperature in Celsius" type="float" value="37" />
                 <param name="sigma" label="Superhelical density Sigma" type="float" value="-0.06" />
                 <param name="salt" label="Salt concentration CNa" type="float" value="0.1" />
-                <param name="small_bubble" label="Smallest bubble size bsizemin" type="float" value="1" />
-                <param name="large_bubble" label="Largest bubble size bsizemax" type="float" value="0" />
-                <param name="bubble_size_step" label="Bubble size step bstep" type="float" value="1" />
+                <param name="small_bubble" label="Smallest bubble size bsizemin" type="integer" value="1" />
+                <param name="large_bubble" label="Largest bubble size bsizemax" type="integer" value="0" />
+                <param name="bubble_size_step" label="Bubble size step bstep" type="integer" value="1" />
                 <param name="threshold" label="Bubble storing threshold" type="float" value="-3.0" />
             </when>
          </conditional>
     </inputs>
+    <configfiles>
+        <configfile name="configfile">
+$getVar('check.temperature', '37')	::Temperature T in Celsius (default 37 C)
+$getVar('check.sigma', '-0.06')	::Superhelical density Sigma (default -0.06)
+$getVar('check.salt', '0.1')	::Salt concentration CNa (default 0.1 M)
+$getVar('check.small_bubble', '1')	::Smallest bubble size bsizemin
+$getVar('check.large_bubble', '0')	::Largest bubble size bsizemax
+$getVar('check.bubble_size_step', '1')	::Bubble size step bstep
+$getVar('check.threshold', '-3.0')	::Bubble storing threshold (default -3)
+        </configfile>
+        <configfile name="enthalpy">
+-12.84	-12.52	-11.58	-13.72
+-13.43	-13.00	-13.72	-15.89
+-11.72	-13.67	-12.84	-13.43
+-13.67	-17.07	-12.52	-13.00
+        </configfile>
+        <configfile name="entropy">
+-11.29	-10.53	-10.16	-11.56
+-11.38	-9.89	-11.56	-12.42
+-10.89	-11.55	-11.29	-11.38
+-11.55	-13.68	-10.53	-9.89
+        </configfile>
+    </configfiles>
     <outputs>
         <data name="outfile1" format="bed" />
         <data name="outfile2" format="bed" />