Mercurial > repos > yufei-luo > s_mart

diff SMART/galaxy/coordinatesToSequence.xml @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/galaxy/coordinatesToSequence.xml	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,68 @@
+<tool id="coordinatesToSequence" name="coordinates to sequence">
+	<description>Coordinates to Sequences: Extract the sequences from a list of coordinates.</description>
+	<requirements>
+		<requirement type="set_environment">PYTHONPATH</requirement>
+	</requirements>
+	<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> 
+	
+	<help>
+You can use this tool, if you just want to convert your mapping data to genomic coordinates, without any filtering. It requires a genomic coordinates file together with its format, an output format (GFF3, BED, etc...), the genome, and prints you the corresponding file.
+	</help>
+</tool>