Mercurial > repos > bernhardlutz > exparna
changeset 3:8c7e7f914a53 draft
Uploaded
author | bernhardlutz |
---|---|
date | Sat, 28 Dec 2013 15:15:22 -0500 |
parents | 414f51a0b5b5 |
children | ee3d71cb8dc8 |
files | create_html.py exparna.xml test-data/input.fasta test-data/input.fasta~ tool_dependencies.xml |
diffstat | 5 files changed, 124 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/create_html.py Sat Dec 28 15:15:22 2013 -0500 @@ -0,0 +1,26 @@ +#!/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()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/exparna.xml Sat Dec 28 15:15:22 2013 -0500 @@ -0,0 +1,59 @@ +<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fasta Sat Dec 28 15:15:22 2013 -0500 @@ -0,0 +1,4 @@ +>AF165050.379 +UUGGGGGCGACAUUCCACCAUAGAUAAUUCCCCUGUGAGGAAUUACUGUUUUAACGCAGAAAGCGUUUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCUUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGAUGACCGGGUCCUUUCUUGGAUCAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUCCUAAACCCCAAAGAAAAACCAAACGUAACACCAACCG +>D45172.391 +GCCAGCCCCCUGAUGGGGGCGACACUCCACCAUAGAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUCUUGGAUCAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUCCAAAACCCCAAAGAAAAAUCAAACGUAACACCAACCG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fasta~ Sat Dec 28 15:15:22 2013 -0500 @@ -0,0 +1,4 @@ +>AF165050.379 +UUGGGGGCGACAUUCCACCAUAGAUAAUUCCCCUGUGAGGAAUUACUGUUUUAACGCAGAAAGCGUUUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCUUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGAUGACCGGGUCCUUUCUUGGAUCAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUCCUAAACCCCAAAGAAAAACCAAACGUAACACCAACCG +>D45172.391 +GCCAGCCCCCUGAUGGGGGCGACACUCCACCAUAGAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUCUUGGAUCAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUCCAAAACCCCAAAGAAAAAUCAAACGUAACACCAACCG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Dec 28 15:15:22 2013 -0500 @@ -0,0 +1,31 @@ +<?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>