Mercurial > repos > bernhardlutz > exparna

--- a/create_html.py	Sat Dec 28 15:09:10 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import sys
-import zipfile
-
-
-os.chdir(sys.argv[2])
-o = open( 'results.html', 'w+' )
-
-
-o.write('<html> <body> <h1> ExpaRNA Result </h1>' )
-
-for filename in os.listdir( sys.argv[2] ):
-    if os.path.isfile( os.path.join( sys.argv[2], filename) ) and False ==(filename.endswith('epm') or filename.endswith('fa') or filename.endswith('aln') or filename.endswith('html')):
-        o.write( '<img src="%s" /><br />' % ( filename ))
-
-o.write( '</body></html>' )
-o.close()
-
-# create zip file
-
-zf = zipfile.ZipFile(sys.argv[1], mode='w')
-for files in os.listdir(sys.argv[2]):
-        zf.write(files)
-zf.close()
--- a/exparna.xml	Sat Dec 28 15:09:10 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-<tool id="exparna" name="ExpaRNA" version="0.1.0">
-    <description></description>
-    <requirements>
-        <requirement type="package" version="1.0">exparna</requirement>
-        <requirement type="set_environment">EXPARNA_SCRIPT_PATH</requirement>
-    </requirements>
-    <command>
-ExpaRNA
--t$emp_scoring
-#if $check == "no":
--n$max_used_sub
-#end if
--s$min_incl_sub
-$locarna_input
-$alignment_to_file
-$list_in_file
-$all_in_file
-$fastafile;
-    mkdir $outfile.files_path;
-    cp ./ExpaRNA-results/* $outfile.files_path;
-    python \$EXPARNA_SCRIPT_PATH/create_html.py $outfile $outfile.files_path;
-    </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="fastafile" type="data" label="Fasta Input File" />
-        <param name="min_incl_sub" label="Minimal size of included substructures" type="integer" value="7" help="-s" />
-        <conditional name="check">
-            <param name="check_all" type="boolean" truevalue="yes" falsevalue="no" label="Use all substructures" help="" checked="true" />
-            <when value="no">
-            <param name="max_used_sub" label="Maximum number of used substructures" type="integer" value="0" help="-n" />
-            </when>
-         </conditional>
-
-        <param name="emp_scoring" type="select" value="no" label="EPM Scoring" help="-t">
-                        <option value="1" selected="true">Default</option>
-                        <option value="2">Prefer Larger Patterns</option>
-        </param>
-        <!-- output parameter alles booleans
-        /!-->
-        <param name="locarna_input" type="boolean" checked="true" truevalue="-i" falsevalue="" label="Write ExpaRNA result as input for LocARNA with anchor constraints" help="-i" />
-        <param name="alignment_to_file" type="boolean" checked="false" truevalue="-o" falsevalue="" label="Write ExpaRNA result as alignment into text file" help="-o" />
-        <param name="list_in_file" type="boolean" checked="false" truevalue="-e" falsevalue="" label="Write ExpaRNA result as list in file" help="-e" />
-        <param name="all_in_file" type="boolean" checked="false" truevalue="-a" falsevalue="" label="Write all EPMs into file" help="-a" />
-    </inputs>
-    <outputs>
-        <data name="outfile" format="zip" />
-    </outputs>
-    <help>**What it does**
-    http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp
-
-ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Instead of computing a full sequence-structure alignment, it computes the best arrangement of sequence-structure motifs common to two RNAs. A motif is a local (or isolated) substructure which is identical to both RNAs. ExpaRNA requires a given nested secondary structure for both RNAs. If no structure is available, RNAfold from Vienna RNA Package is used for a structure prediction. The accuracy of the algorithm is mainly controlled by the minimal size of the included sequence-structure motifs. ExpaRNA is especially useful for comparative structural RNA analysis and to speed-up complex sequence-structure alignment methods. For this purpose, the predicted common substructures by ExpaRNA are used as anchor constraints for a full structural alignment.
-
-    **Output**
-    You will receive a zip file containing all output files
-    </help>
-</tool>
--- a/test-data/input.fasta	Sat Dec 28 15:09:10 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
->AF165050.379
-UUGGGGGCGACAUUCCACCAUAGAUAAUUCCCCUGUGAGGAAUUACUGUUUUAACGCAGAAAGCGUUUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCUUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGAUGACCGGGUCCUUUCUUGGAUCAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUCCUAAACCCCAAAGAAAAACCAAACGUAACACCAACCG
->D45172.391
-GCCAGCCCCCUGAUGGGGGCGACACUCCACCAUAGAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUCUUGGAUCAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUCCAAAACCCCAAAGAAAAAUCAAACGUAACACCAACCG
--- a/test-data/input.fasta~	Sat Dec 28 15:09:10 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
->AF165050.379
-UUGGGGGCGACAUUCCACCAUAGAUAAUUCCCCUGUGAGGAAUUACUGUUUUAACGCAGAAAGCGUUUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCUUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGAUGACCGGGUCCUUUCUUGGAUCAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUCCUAAACCCCAAAGAAAAACCAAACGUAACACCAACCG
->D45172.391
-GCCAGCCCCCUGAUGGGGGCGACACUCCACCAUAGAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUCUUGGAUCAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUCCAAAACCCCAAAGAAAAAUCAAACGUAACACCAACCG
--- a/tool_dependencies.xml	Sat Dec 28 15:09:10 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="vienna_rna" version="1.8.5">
-        <repository changeset_revision="53e25262a701" name="package_vienna_rna_1_8" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="exparna" version="1.0">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://www.bioinf.uni-freiburg.de/Software/expaRNA/exparna-1.0.tar.gz</action>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="53e25262a701" name="package_vienna_rna_1_8" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="vienna_rna" version="1.8.5" />
-                    </repository>
-                </action>
-                <action type="shell_command">./configure --prefix $INSTALL_DIR --with-RNA=$ROOT_VIENNA_RNA_DIR</action>
-                <action type="make_install" />
-                <action type="move_file">
-                    <source>create_html.py</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="set" name="EXPARNA_SCRIPT_PATH">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>Compiling ExpaRNA requires a C compiler (typically gcc)</readme>
-    </package>
-</tool_dependency>