Mercurial > repos > yufei-luo > s_mart

diff smart_toolShed/SMART/galaxy/coordinatesToSequence.xml @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/galaxy/coordinatesToSequence.xml	Thu Jan 17 10:52:14 2013 -0500
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+<tool id="coordinatesToSequence" name="coordinates to sequence">
+	<description>Coordinates to Sequences: Extract the sequences from a list of coordinates.</description>
+	<command interpreter="python">
+		../Java/Python/coordinatesToSequence.py -i $formatType.inputFileName1
+		#if $formatType.FormatInputFileName1 == 'bed':
+			-f bed
+		#elif $formatType.FormatInputFileName1 == 'gff':
+			-f gff	
+		#elif $formatType.FormatInputFileName1 == 'gff2':
+			-f gff2
+		#elif $formatType.FormatInputFileName1 == 'gff3':
+			-f gff3
+		#elif $formatType.FormatInputFileName1 == 'sam':
+			-f sam
+		#elif $formatType.FormatInputFileName1 == 'gtf':
+			-f gtf
+		#end if
+			
+		-s $sequence
+		-o $outputFileFasta
+		
+	</command>
+
+	<inputs>
+		<conditional name="formatType">
+			<param name="FormatInputFileName1" type="select" label="Input File Format">
+				<option value="bed">bed</option>
+				<option value="gff">gff</option>
+				<option value="gff2">gff2</option>
+				<option value="gff3">gff3</option>
+				<option value="sam">sam</option>
+				<option value="gtf">gtf</option>
+			</param>
+			<when value="bed">
+				<param name="inputFileName1" format="bed" type="data" label="Input File"/>
+			</when>
+			<when value="gff">
+				<param name="inputFileName1" format="gff" type="data" label="Input File"/>
+			</when>
+			<when value="gff2">
+				<param name="inputFileName1" format="gff2" type="data" label="Input File"/>
+			</when>
+			<when value="gff3">
+				<param name="inputFileName1" format="gff3" type="data" label="Input File"/>
+			</when>
+			<when value="sam">
+				<param name="inputFileName1" format="sam" type="data" label="Input File"/>
+			</when>
+			<when value="gtf">
+				<param name="inputFileName1" format="gtf" type="data" label="Input File"/>
+			</when>
+		</conditional>
+
+ 	    <param name="sequence" type="data" label="Reference fasta File" format="fasta"/>
+
+	</inputs>
+
+	<outputs>
+		<data name="outputFileFasta" format="fasta" label="coordinates to sequences output"/>
+	</outputs> 
+	
+</tool>