-Galaxy Tool wrapper for UNAFold

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This is the Galaxy wrapper for the UNAFold. UNAFold software was developed for nucleic acid folding and hybridization prediction (doi: 10.1007/978-1-60327-429-6_1, doi: 10.1093/nar/gki591). This wrapper is not yet deposited in the Tool-Shed repository, so this is the single place where it can downloaded.

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-Installation

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Save UNAFold.pl in your $PATH, that is accesable to the Galaxy.
Create the directory unafold in $GALAXY_DIR/tools/ and copy unafold.xml and unafold.sh files into it.
Add the Galaxy tool definition to the tools_conf.xml:

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    <section id="unafold_tool" name="UNAFold">
-        <tool file="unafold/unafold.xml" />
-    </section>`

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Please, be sure that zip datatype is registered in your Galaxy instance. If not, add the following string to the datatypes_conf.xml file:

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    <datatype extension="zip" type="galaxy.datatypes.binary:Binary" mimetype="application/zip" subclass="True" />

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Reload the Galaxy instance.

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	#!/bin/bash
	set -e
	-
	#arguments are -i input sequence file in fasta
	# -o output zip arhive
	# -t temp directory with results
	# -a DNA\|RNA
	# -c tempreature (C)
	# -s [Na+] in M
	# -m [Mg++] in M
	# -b maxbp
	-
	#-n, --NA=(RNA \| DNA) (defaults to RNA)
	#-t, --temp=<temperature> (defaults to 37)
	#-N, --sodium=<[Na+] in M> (defaults to 1)
	#-M, --magnesium=<[Mg++] in M> (defaults to 0)
	#-p, --polymer
	#-C, --Ct=<total strand concentration>
	#-I, --noisolate
	#-m, --maxbp=<maximum basepair distance>
	#-c, --constraints=<name of constraints file> (defaults to prefix.aux)
	#-P, --percent=<energy increment percent> (defaults to 5)
	#-W, --window=<window size> (default set by sequence length)
	#-X, --max=<maximum number of foldings> (defaults to 100)
	# --ann=(none \| p-num \| ss-count) (defaults to none)
	# --mode=(auto \| bases \| lines) (defaults to auto)
	# --label=<base numbering frequency>
	# --rotate=<structure rotation angle>
	# --run-type=(text \| html) (defaults to text)
	# --model=(EM \| PF) (defaults to EM)
	# --circular
	#Obscure options:
	# --allpairs
	# --maxloop=<maximum bulge/interior loop size> (defaults to 30)
	# --nodangle
	# --simple
	# --prefilter=<filter value>
	-
	NA=RNA
	TM=37
	NAT=1
	MG=0
	-
	while getopts ":i:o:t:a:c:s:m:" OPTION;
	do
	case $OPTION in
	i) INPUT="$OPTARG";;
	o) ZIP_ARHIVE="$OPTARG";;
	t) TEMP_DIR="$OPTARG";;
	a) NA="$OPTARG";;
	c) TM="$OPTARG";;
	s) NAT="$OPTARG";;
	m) MG="$OPTARG";;
	esac
	done

	mkdir -p ${TEMP_DIR}/unafold
	cd ${TEMP_DIR}/unafold
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	NA=$(echo $NA \| tr '[:lower:]' '[:upper:]')
	-
	# calucalation of RNA don't need the concentraion of salts
	if [[ ${NA} == 'DNA' ]]; then
	UNAFold.pl -n ${NA} -t ${TM} -N ${NAT} -M ${MG} ${INPUT}
	else
	UNAFold.pl -n ${NA} -t ${TM} ${INPUT}
	fi
	-
	echo ""
	echo "Parametres of UNAFold run:"
	cat *run
	-
	cd ../
	zip -r -q unafold.zip unafold
	mv unafold.zip ${ZIP_ARHIVE}
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	<?xml version="1.0"?>
	<tool id="unafold_1" name="unafold" version="0.0.1">
	<description>Folding of RNA sequences using UNAFold</description>
	<command interpreter="bash">
	unafold.sh -i $inputFastaFile -o $outputArhive -t '$outputArhive.extra_files_path' -a ${ na_type.nucacid } -c $tmp
	#if str($na_type.nucacid) == 'dna':
	-s ${ na_type.sodium } -m ${ na_type.magnesium }
	#end if
	> $outputLog
	</command>
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	<inputs>
	<param format="fasta" name="inputFastaFile" type="data" label="Fasta input file"/>
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	<conditional name="na_type">
	<param name="nucacid" type="select" label="Nucleic Acid Type">
	<option value="rna" selected="true">RNA</option>
	<option value="dna">DNA</option>
	</param>
	<when value="dna">
	<param name="sodium" type="float" size="6" value="1.0" min="0" max="100" label="[Na+] in M"/>
	<param name="magnesium" type="float" size="6" value="0.0" min="0" max="100" label="[Mg++] in M"/>
	</when>
	<when value="rna">
	<!-- do nothing here -->
	</when>
	</conditional>
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	<param name="tmp" type="integer" size="3" value="37" min="0" max="100" label="Temperature (C)"/>
	-
	</inputs>
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	<outputs>
	<data format="zip" name="outputArhive" label="Arhive: UNAFold on $on_string"/>
	<data format="txt" name="outputLog" label="Log: UNAFold on $on_string"/>
	</outputs>
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	<help>
	-
	This tool computes the fold of RNA/DNA using UNAFold v.3.8.
	-
	UNAFold (http://mfold.rna.albany.edu/?q=unafold-man-pages) is a comprehensive software package for nucleic acid folding and hybridization prediction. The name is derived from "Unified Nucleic Acid Folding". Folding of single-stranded RNA or DNA, or hybridization between two single-strands, is accomplished in a variety of ways. Partition functions can be computed to derive base pair probabilities and stochastic samples of foldings or hybridizations. Energy minimization methods compute minimum free energy foldings or hybridizations, and can also compute suboptimal foldings that mimic the performance of the famous mfold software.
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	For melting simulations, the package computes not just melting temperatures, but entire melting profiles. UV absorbance at 260 nm, heat capacity change (Cp), and mole fractions of different molecular species are computed as a function of temperature. ITC (Isothermal Titration Calorimetry) and van't Hoff plots are also simulated.
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	UNAFold v.3.8 (http://mfold.rna.albany.edu/?q=unafold-man-pages)
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	Galaxy wrapper for UNAFold v. 0.0.1
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	Author: Sergei Ryazansky, s.ryazansky@gmail.com
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	Web-site: https://github.com/DrHogart/galaxy-tools-unafold)
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	-
	</help>
	</tool>
	-

- - DrHogart/galaxy-tools-unafold + GNU GENERAL PUBLIC LICENSE + TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION - - - - -

HTTPS clone URL

Subversion checkout URL

Users who have contributed to this file

- - DrHogart/galaxy-tools-unafold - - - - - -

HTTPS clone URL

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-Galaxy Tool wrapper for UNAFold

-Installation

- - DrHogart/galaxy-tools-unafold - - - - - -

HTTPS clone URL

Subversion checkout URL

Users who have contributed to this file

- - DrHogart/galaxy-tools-unafold + + - - - - -

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	-
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