Mercurial > repos > yufei-luo > s_mart

diff SMART/galaxy/restrictFromSize.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/restrictFromSize.xml	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,102 @@
+<tool id="restrictFromSize" name="restrict from size">
+	<description>Select the elements of a list of sequences or transcripts with a given size.</description>
+	<requirements>
+		<requirement type="set_environment">PYTHONPATH</requirement>
+	</requirements>
+	<command interpreter="python">
+		../Java/Python/restrictFromSize.py -i $formatType.inputFileName
+		#if $formatType.FormatInputFileName == 'fasta':
+			-f fasta
+		#elif $formatType.FormatInputFileName == 'bed':
+			-f bed
+		#elif $formatType.FormatInputFileName == 'gff':
+			-f gff
+		#elif $formatType.FormatInputFileName == 'gff2':
+			-f gff2
+		#elif $formatType.FormatInputFileName == 'gff3':
+			-f gff3
+		#elif $formatType.FormatInputFileName == 'sam':
+			-f sam
+		#elif $formatType.FormatInputFileName == 'gtf':
+			-f gtf
+		#end if
+
+		#if $OptionMax.maximum == "Yes":
+			-M $OptionMax.max
+		#end if		
+		#if $OptionMin.minimum == "Yes":
+			-m $OptionMin.min
+		#end if	
+				
+		-o $outputFileGff 
+	</command>
+
+	<inputs>
+		<conditional name="formatType">
+			<param name="FormatInputFileName" type="select" label="Input File Format">
+				<option value="fasta">fasta</option>
+				<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="fasta">
+				<param name="inputFileName" format="fasta" type="data" label="Input File"/>
+			</when>
+			<when value="bed">
+				<param name="inputFileName" format="bed" type="data" label="Input File"/>
+			</when>
+			<when value="gff">
+				<param name="inputFileName" format="gff" type="data" label="Input File"/>
+			</when>
+			<when value="gff2">
+				<param name="inputFileName" format="gff2" type="data" label="Input File"/>
+			</when>
+			<when value="gff3">
+				<param name="inputFileName" format="gff3" type="data" label="Input File"/>
+			</when>
+			<when value="sam">
+				<param name="inputFileName" format="sam" type="data" label="Input File"/>
+			</when>
+			<when value="gtf">
+				<param name="inputFileName" format="gtf" type="data" label="Input File"/>
+			</when>
+		</conditional>
+		
+		<conditional name="OptionMax">
+			<param name="maximum" type="select" label="maximum number of np">
+				<option value="Yes">Yes</option>
+				<option value="No" selected="true">No</option>
+			</param>
+			<when value="Yes">
+				<param name="max" type="integer" value="1" help="Be Careful! The value must be upper than 0"/>
+			</when>
+			<when value="No">
+			</when>
+		</conditional>
+		
+		<conditional name="OptionMin">
+			<param name="minimum" type="select" label="minimum number of np">
+				<option value="Yes">Yes</option>
+				<option value="No" selected="true">No</option>
+			</param>
+			<when value="Yes">
+				<param name="min" type="integer" value="1" help="Be Careful! The value must be upper than 0"/>
+			</when>
+			<when value="No">
+			</when>
+		</conditional>	
+		
+	</inputs>
+
+	<outputs>
+		<data name="outputFileGff" format="gff3" label="[restrict from size] output file"/>
+	</outputs> 
+	
+	<help>
+Reads a list of sequences or genomic coordinates and outputs those which are longer and / or shorter than a given size ---which you provide.
+	</help>
+
+</tool>