Mercurial > repos > yufei-luo > s_mart

changeset 17:b0e8584489e6

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Deleted selected files
author m-zytnicki
date Mon, 22 Apr 2013 11:11:10 -0400
parents 6135c3075bc5
children 94ab73e8a190
files SMART/galaxy/cleanGff.xml SMART/galaxy/clusterize.xml SMART/galaxy/getSequence.xml
diffstat 3 files changed, 0 insertions(+), 99 deletions(-) [+]
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--- a/SMART/galaxy/cleanGff.xml	Mon Apr 22 11:09:41 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-<tool id="cleanGff" name="clean Gff">
-	  <description>Clean a GFF file (e.g. as given by NCBI) and produces a new GFF3 file, understood by S-MART.</description>
-	  <command interpreter="python"> ../Java/Python/cleanGff.py -i $inputFile 
-		  -t $type 
-		  -o $outputFile
-	  </command>
-
-	      <inputs>
-		      <param name="inputFile" type="data" label="Input File" format="gff"/>
-		      <param name="type" type="text" value="tRNA,rRNA,ncRNA,CDS" label="Tags you keep" help="lists of comma separated types that you want to keep, e.g. ncRNA,tRNA,rRNA,CDS"/>
-	      </inputs>
-
-	      <outputs>
-	          <data format="gff3" name="outputFile" label="[cleanGff] Output File"/>
-	      </outputs>
-
-	<help>
-		A GFF file (please consult http://www.sequenceontology.org/gff3.shtml to know more about it) may contain different sources of information: chromosome size, genes, transcripts, etc. S-MART mostly works on transcripts. This scripts filters the input GFF3 to keep the information you really want, based on the feature (3rd column).
-	</help>
-</tool>
-
--- a/SMART/galaxy/clusterize.xml	Mon Apr 22 11:09:41 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-<tool id="MergingDataClusterize" name="Clusterize">
-	<description>Clusterize features when their genomic intervals overlap.</description>
-	<command interpreter="python">
-		../Java/Python/clusterize.py -i $formatType.inputFileName
-		#if $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
-		#end if
-		-o $outputFileGff 
-		$colinear
-		$normalize
-		-d $distance
-		$log $outputFileLog
-	</command>
-
-	<inputs>
-		<conditional name="formatType">
-			<param name="FormatInputFileName" 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>
-			</param>
-			<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>
-		</conditional>
-
-		<param name="colinear" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Only merge collinear data"/>
-		<param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Normalize data." help="This only works if the tag nbOccurrences is set."/>
-		<param name="distance" type="integer" value="0" label="Merge features if their relative distance is withing N nt"/>
-	</inputs>
-
-	<outputs>
-		<data name="outputFileGff" format="gff3" label="[clusterize]output file"/>
-	</outputs> 
-</tool>
--- a/SMART/galaxy/getSequence.xml	Mon Apr 22 11:09:41 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-<tool id="getSequence" name="get sequence">
-  <description>Get a single sequence in a FASTA file.</description>
-  <command interpreter="python"> ../Java/Python/getSequence.py -i $inputFile 
-	-n $name
-  	-o $outputFile  
-  
-  </command>
-  
-  
-  <inputs>
-    <param name="inputFile" type="data" label="Input fasta File" format="fasta"/>
-  	<param name="name" type="text" value="None" label="name of the sequence [compulsory option]"/>
-  </inputs>
-
-  <outputs>
-    <data format="fasta" name="outputFile" label="[getSequence] Output File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>