changeset 16:6135c3075bc5

Deleted selected files
author m-zytnicki
date Mon, 22 Apr 2013 11:09:41 -0400
parents 440ceca58672
children b0e8584489e6
files SMART/galaxy/ConvertTranscriptFile_BedToCsv.xml SMART/galaxy/ConvertTranscriptFile_BedToGff2.xml SMART/galaxy/ConvertTranscriptFile_BedToGff3.xml SMART/galaxy/ConvertTranscriptFile_BedToSam.xml SMART/galaxy/ConvertTranscriptFile_BlastToCsv.xml SMART/galaxy/ConvertTranscriptFile_BlastToGff2.xml SMART/galaxy/ConvertTranscriptFile_BlastToGff3.xml SMART/galaxy/ConvertTranscriptFile_BlastToSam.xml SMART/galaxy/ConvertTranscriptFile_FastqToFasta.xml SMART/galaxy/ConvertTranscriptFile_Gff2ToCsv.xml SMART/galaxy/ConvertTranscriptFile_Gff2ToGff3.xml SMART/galaxy/ConvertTranscriptFile_Gff2ToSam.xml SMART/galaxy/ConvertTranscriptFile_Gff3ToCsv.xml SMART/galaxy/ConvertTranscriptFile_Gff3ToGff2.xml SMART/galaxy/ConvertTranscriptFile_Gff3ToSam.xml SMART/galaxy/ConvertTranscriptFile_Gff3ToWig.xml SMART/galaxy/ConvertTranscriptFile_SamToCsv.xml SMART/galaxy/ConvertTranscriptFile_SamToGff2.xml SMART/galaxy/ConvertTranscriptFile_SamToGff3.xml SMART/galaxy/FindOverlaps_optim.xml SMART/galaxy/findTss.xml SMART/galaxy/getNb.xml SMART/galaxy/mappingToCoordinates.xml SMART/galaxy/modifyFasta.xml SMART/galaxy/plot.xml SMART/galaxy/plotRepartition.xml SMART/galaxy/qualToFastq.xml SMART/galaxy/restrictSequenceList.xml SMART/galaxy/testArgum.xml SMART/galaxy/testR.xml SMART/galaxy/trimAdaptor.xml
diffstat 31 files changed, 0 insertions(+), 795 deletions(-) [+]
line wrap: on
line diff
--- a/SMART/galaxy/ConvertTranscriptFile_BedToCsv.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="ConvertTranscriptFile_BedToCsv" name="Bed -> Csv">
-  <description>Convert Bed File to Csv File.</description>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f bed -o $outputFile -g csv yes 2>$logFile </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="bed"/>
-  </inputs>
-
-  <outputs>
-    <data format="csv" name="outputFile" label="[bed -> csv] Output File"/>
-    <data format="txt" name="logFile" label="[bed -> csv] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/ConvertTranscriptFile_BedToGff2.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="ConvertTranscriptFile_BedToGff2" name="Bed -> Gff2">
-  <description>Convert Bed File to Gff2 File.</description>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f bed -o $outputFile -g gff yes 2>$logFile </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="bed"/>
-  </inputs>
-
-  <outputs>
-    <data format="gff" name="outputFile" label="[bed -> gff2] Output File"/>
-    <data format="txt" name="logFile" label="[bed -> gff2] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/ConvertTranscriptFile_BedToGff3.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="ConvertTranscriptFile_BedToGff3" name="Bed -> Gff3">
-  <description>Convert Bed File to Gff3 File.</description>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f bed -o $outputFile -g gff3 yes 2>$logFile </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="bed"/>
-  </inputs>
-
-  <outputs>
-    <data format="gff3" name="outputFile" label="[bed -> gff3] Output File"/>
-    <data format="txt" name="logFile" label="[bed -> gff3] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/ConvertTranscriptFile_BedToSam.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="ConvertTranscriptFile_BedToSam" name="Bed -> Sam">
-  <description>Convert Bed File to Sam File.</description>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f bed -o $outputFile -g sam yes 2>$logFile </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="bed"/>
-  </inputs>
-
-  <outputs>
-    <data format="sam" name="outputFile" label="[bed -> sam] Output File"/>
-    <data format="txt" name="logFile" label="[bed -> sam] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/ConvertTranscriptFile_BlastToCsv.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="ConvertTranscriptFile_BlastToCsv" name="Blast (-m 8) -> Csv">
-  <description>Convert Blast (-m 8) File to Csv File.</description>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f blast -o $outputFile -g csv yes 2>$logFile </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="tabular"/>
-  </inputs>
-
-  <outputs>
-    <data format="csv" name="outputFile" label="[blast -> csv] Output File"/>
-    <data format="txt" name="logFile" label="[blast -> csv] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/ConvertTranscriptFile_BlastToGff2.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="ConvertTranscriptFile_BlastToGff2" name="Blast (-m 8) -> Gff2">
-  <description>Convert Blast (-m 8) File to Gff2 File.</description>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f blast -o $outputFile -g gff2 yes 2>$logFile </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="tabular"/>
-  </inputs>
-
-  <outputs>
-    <data format="gff" name="outputFile" label="[blast -> gff2] Output File"/>
-    <data format="txt" name="logFile" label="[blast -> gff2] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/ConvertTranscriptFile_BlastToGff3.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="ConvertTranscriptFile_BlastToGff3" name="Blast (-m 8) -> Gff3">
-  <description>Convert Blast (-m 8) File to Gff3 File.</description>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f blast -o $outputFile -g gff3 yes 2>$logFile </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="tabular"/>
-  </inputs>
-
-  <outputs>
-    <data format="gff3" name="outputFile" label="[blast -> gff3] Output File"/>
-    <data format="txt" name="logFile" label="[blast -> gff3] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/ConvertTranscriptFile_BlastToSam.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="ConvertTranscriptFile_BlastToSam" name="Blast (-m 8) -> Sam">
-  <description>Convert Blast (-m 8) File to Sam File.</description>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f blast -o $outputFile -g sam yes 2>$logFile </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="tabular"/>
-  </inputs>
-
-  <outputs>
-    <data format="sam" name="outputFile" label="[blast -> sam] Output File"/>
-    <data format="txt" name="logFile" label="[blast -> sam] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/ConvertTranscriptFile_FastqToFasta.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="ConvertTranscriptFile_FastqToFasta" name="Fastq -> Fasta">
-  <description>Convert Fastq File to Fasta File.</description>
-  <command interpreter="python"> ../Java/Python/fastqToFasta.py -i $inputFile -o $outputFile 2>$logFile </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="fastq"/>
-  </inputs>
-
-  <outputs>
-    <data format="fasta" name="outputFile" label="[fastq -> fasta] Output File"/>
-    <data format="txt" name="logFile" label="[fastq -> fasta] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/ConvertTranscriptFile_Gff2ToCsv.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="ConvertTranscriptFile_Gff2ToCsv" name="Gff2 -> Csv">
-  <description>Convert Gff2 File to Csv File.</description>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f gff2 -o $outputFile -g csv yes 2>$logFile </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="gff"/>
-  </inputs>
-
-  <outputs>
-    <data format="csv" name="outputFile" label="[gff2 -> csv] Output File"/>
-    <data format="txt" name="logFile" label="[gff2 -> csv] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/ConvertTranscriptFile_Gff2ToGff3.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="ConvertTranscriptFile_Gff2ToGff3" name="Gff2 -> Gff3">
-  <description>Convert Gff2 File to Gff3 File.</description>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f gff2 -o $outputFile -g gff3 yes 2>$logFile </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="gff"/>
-  </inputs>
-
-  <outputs>
-    <data format="gff3" name="outputFile" label="[gff2 -> gff3] Output File"/>
-    <data format="txt" name="logFile" label="[gff2 -> gff3] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/ConvertTranscriptFile_Gff2ToSam.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="ConvertTranscriptFile_Gff2ToSam" name="Gff2 -> Sam">
-  <description>Convert Gff2 File to Sam File.</description>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f gff2 -o $outputFile -g sam yes 2>$logFile </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="gff"/>
-  </inputs>
-
-  <outputs>
-    <data format="sam" name="outputFile" label="[gff2 -> sam] Output File"/>
-    <data format="txt" name="logFile" label="[gff2 -> sam] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/ConvertTranscriptFile_Gff3ToCsv.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="ConvertTranscriptFile_Gff3ToCsv" name="Gff3 -> Csv">
-  <description>Convert Gff3 File to Csv File.</description>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f gff3 -o $outputFile -g csv yes 2>$logFile </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="gff3"/>
-  </inputs>
-
-  <outputs>
-    <data format="csv" name="outputFile" label="[gff3 -> csv] Output File"/>
-    <data format="txt" name="logFile" label="[gff3 -> csv] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/ConvertTranscriptFile_Gff3ToGff2.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="ConvertTranscriptFile_Gff3ToGff2" name="Gff3 -> Gff2">
-  <description>Convert Gff3 File to Gff2 File.</description>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f gff3 -o $outputFile -g gff2 yes 2>$logFile </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="gff3"/>
-  </inputs>
-
-  <outputs>
-    <data format="gff" name="outputFile" label="[gff3 -> gff2] Output File"/>
-    <data format="txt" name="logFile" label="[gff3 -> gff2] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/ConvertTranscriptFile_Gff3ToSam.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="ConvertTranscriptFile_Gff3ToSam" name="Gff3 -> Sam">
-  <description>Convert Gff3 File to Sam File.</description>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f gff3 -o $outputFile -g sam yes 2>$logFile </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="gff3"/>
-  </inputs>
-
-  <outputs>
-    <data format="sam" name="outputFile" label="[gff3 -> sam] Output File"/>
-    <data format="txt" name="logFile" label="[gff3 -> sam] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/ConvertTranscriptFile_Gff3ToWig.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="ConvertTranscriptFile_Gff3ToWig" name="Gff3 -> Wig">
-  <description>Convert Gff3 File to Wig File.</description>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f gff3 -o $outputFile -g wig yes 2>$logFile </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="gff3"/>
-  </inputs>
-
-  <outputs>
-    <data format="wig" name="outputFile" label="[gff3 -> wig] Output File"/>
-    <data format="txt" name="logFile" label="[gff3 -> wig] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
\ No newline at end of file
--- a/SMART/galaxy/ConvertTranscriptFile_SamToCsv.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="ConvertTranscriptFile_SamToCsv" name="Sam -> Csv">
-  <description>Convert Sam File to Csv File.</description>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f sam -o $outputFile -g csv yes 2>$logFile </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="sam"/>
-  </inputs>
-
-  <outputs>
-    <data format="csv" name="outputFile" label="[sam -> csv] Output File"/>
-    <data format="txt" name="logFile" label="[sam -> csv] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/ConvertTranscriptFile_SamToGff2.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="ConvertTranscriptFile_SamToGff2" name="Sam -> Gff2">
-  <description>Convert Sam File to Gff2 File.</description>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f sam -o $outputFile -g gff2 yes 2>$logFile </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="sam"/>
-  </inputs>
-
-  <outputs>
-    <data format="gff" name="outputFile" label="[sam -> gff2] Output File"/>
-    <data format="txt" name="logFile" label="[sam -> gff2] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/ConvertTranscriptFile_SamToGff3.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="ConvertTranscriptFile_SamToGff3" name="Sam -> Gff3">
-  <description>Convert Sam File to Gff3 File.</description>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f sam -o $outputFile -g gff3 yes 2>$logFile </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="sam"/>
-  </inputs>
-
-  <outputs>
-    <data format="gff3" name="outputFile" label="[sam -> gff3] Output File"/>
-    <data format="txt" name="logFile" label="[sam -> gff3] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/FindOverlaps_optim.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-<tool id="findOverlaps" name="findOverlaps">
-	<description>Finds the overlapped reference reads.</description>
-	<command interpreter="python">
-		../Java/Python/FindOverlaps_optim.py -i $inputRef -j $inputQ -o $outputFileGff 
-	</command>
-	
-  <inputs>
-    <param name="inputRef" type="data" label="Input Reference File" format="gff3"/>
-    <param name="inputQ" type="data" label="Input Query File" format="gff3"/>
-  </inputs>
-
-	<outputs>
-		<data name="outputFileGff" format="gff3"/>
-	</outputs> 
-	
-</tool>
\ No newline at end of file
--- a/SMART/galaxy/findTss.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-<tool id="findTss" name="findTss">
-	<description>Find the transcription start site of a list of transcripts.</description>
-	<command interpreter="python">
-		../Java/Python/findTss.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
-		#end if
-			
-
-		-o $outputFileGff 
-		$colinear
-		$normalize
-		-d $distance
-		$excel $excelOutput
-		
-	</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>
-			</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>
-		</conditional>
-
-		<param name="colinear" type="boolean" truevalue="-e" falsevalue="" checked="false" label="colinear option" help="This option clusterizes only the same strand reads"/>
-		<param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="normalize option for only GFF3 file format" help="This option normalize (Warning!! Only for GFF3 file!!!!!)"/>
-		<param name="distance" type="text" value="10" label="distance option" help="Limit the maximum distance between two reads"/>
-		<param name="excel" type="boolean" truevalue="-c" falsevalue="" checked="false" label="excel option" help="This option creates a csv file."/>
-	</inputs>
-
-	<outputs>
-		<data name="outputFileGff" format="gff3" label="[findTss] Output File"/>
-		<data name="excelOutput" format="csv" label="[findTss] CSV File">
-			<filter>excel</filter>
-		</data>	
-	</outputs> 
-	
-</tool>
--- a/SMART/galaxy/getNb.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,78 +0,0 @@
-<tool id="getNumber" name="get number">
-	<description>Get the distribution of exons per transcripts, or mapping per read, or transcript per cluster.</description>
-	<command interpreter="python">
-		../Java/Python/getNb.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
-		#elif $formatType.FormatInputFileName == 'gtf':
-			-f gtf
-		#end if
-		-o $outputFilePNG
-		-q $query
-		$barPlot
-		#if $optionXMAX.XMAX == 'Yes':
-			-x $optionXMAX.xMaxValue
-		#end if		
-
-	</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>
-				<option value="gtf">gtf</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>
-			<when value="gtf">
-				<param name="inputFileName" format="gtf" type="data" label="Input File"/>
-			</when>
-		</conditional>
-		
-		<param name="query" type="text" value="None" label="compulsory option, choice (exon, transcript, cluster)" />
-		<param name="barPlot" type="boolean" truevalue="-b" falsevalue="" checked="false" label="use barplot representation"/>
-		
-		<conditional name="optionXMAX">
-			<param name="XMAX" type="select" label="maximum value on the x-axis to plot ">
-					<option value="Yes">Yes</option>
-					<option value="No" selected="true">No</option>
-			</param>
-			<when value="Yes">
-				<param name="xMaxValue" type="integer" value="0" />
-			</when>
-			<when value="No">
-			</when>
-		</conditional>
-		
-	</inputs>
-
-	<outputs>
-		<data name="outputFilePNG" format="png" label="[getNB]out file"/>
-	</outputs> 
-	
-</tool>
--- a/SMART/galaxy/mappingToCoordinates.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-<tool id="mappingToCoordinates" name="mapping to coordinates">
-	<description>Converts a mapping type file(given by a mapping tool) to a GFF3 type file.</description>
-	<command interpreter="python">
-		../Java/Python/mappingToCoordinates.py -i $formatType.inputFileName
-		#if $formatType.FormatInputFileName == 'bed':
-			-f bed
-		#elif $formatType.FormatInputFileName == 'sam':
-			-f sam
-		#elif $formatType.FormatInputFileName == 'blast -8'
-			-f blast
-		#elif $formatType.FormatInputFileName == 'gff':
-			-f gff	
-		#elif $formatType.FormatInputFileName == 'gff2':
-			-f gff2
-		#elif $formatType.FormatInputFileName == 'gff3':
-			-f gff3
-		#end if
-
-		-o $outputFileGff 
-	</command>
-
-	<inputs>
-		<conditional name="formatType">
-			<param name="FormatInputFileName" type="select" label="Input File Format">
-				<option value="bed">bed</option>
-				<option value="sam">sam</option>
-				<option value="blast -8">blast</option>
-				<option value="gff">gff</option>
-				<option value="gff2">gff2</option>
-				<option value="gff3">gff3</option>
-			</param>
-			<when value="bed">
-				<param name="inputFileName" format="bed" type="data" label="Input File"/>
-			</when>
-			<when value="sam">
-				<param name="inputFileName" format="sam" type="data" label="Input File"/>
-			</when>
-			<when value="blast -8">
-				<param name="inputFileName" format="blast" 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>
-		</conditional>
-	</inputs>
-
-	<outputs>
-		<data name="outputFileGff" format="gff3"/>
-	</outputs> 
-	
-</tool>
--- a/SMART/galaxy/modifyFasta.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-<tool id="modifyFasta" name="modify fasta">
-  <description>Extend or shring a list of sequences.</description>
-  <command interpreter="python"> ../Java/Python/modifyFasta.py -i $inputFile 
-  	#if $OptionStart.start == "Yes":
-			-s $OptionStart.startValue
-  	#end if
-  	
-  	#if $OptionEnd.end == "Yes":
-			-e $OptionEnd.endValue
-  	#end if
-  	-o $outputFile  
-  
-  </command>
-  
-  
-  <inputs>
-    <param name="inputFile" type="data" label="Input fasta File" format="fasta"/>
-	<conditional name="OptionStart">
-			<param name="start" type="select" label="keep first nucleotides">
-				<option value="Yes">Yes</option>
-				<option value="No" selected="true">No</option>
-			</param>
-			<when value="Yes">
-				<param name="startValue" type="integer" value="0"/>
-			</when>
-			<when value="No">
-			</when>
-	</conditional>
-		
-	<conditional name="OptionEnd">
-			<param name="end" type="select" label="keep last nucleotides">
-				<option value="Yes">Yes</option>
-				<option value="No" selected="true">No</option>
-			</param>
-			<when value="Yes">
-				<param name="endValue" type="integer" value="0"/>
-			</when>
-			<when value="No">
-			</when>
-	</conditional>   
-  </inputs>
-
-  <outputs>
-    <data format="fasta" name="outputFile" label="[modifyFasta] Output File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/plot.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-<tool id="plot" name="Plot">
-	<description>Plot some information from a list of transcripts.</description>
-	<command interpreter="python">
-		../Java/Python/plot.py -i $formatType.inputFileName
-		#if $formatType.FormatInputFileName == 'gff':
-			-f gff
-		#elif $formatType.FormatInputFileName == 'gff2':
-			-f gff2
-		#elif $formatType.FormatInputFileName == 'gff3':
-			-f gff3
-		#end if
-		
-		-x $xLabel
-		
-                -y $yLabel
-
-	        -X $XVal
-                -Y $YVal
-
-	        #if $optionLog.log == 'Yes' :
-		    -l $optionLog.logOnAxisLabel
-                #end if
-                
-                -s $shape
-		-o $outputFile
-
-	</command>
-
-	<inputs>
-		<conditional name="formatType">
-			<param name="FormatInputFileName" type="select" label="Input File Format">
-				<option value="gff">gff</option>
-				<option value="gff2">gff2</option>
-				<option value="gff3">gff3</option>
-			</param>
-			<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>
-		</conditional>
-		
-		<param name="xLabel" type="text" value="value1" label="x label option" help="Choose one of the tags of 9th column in GFF file to be plotted as X-axis. Warning: You can only choose the tag value is digital."/>
-                <param name="yLabel" type="text" value="value2" label="y label option" help="Choose one of the tags of 9th column in GFF file to be plotted as Y-axis. You can only choose the tag value is digital."/>
-                <param name="XVal" type="float" value="0.0" label="value for x when tag is not present "/>
-		
-		<param name="YVal" type="float" value="0.0" label="value for y when tag is not present"/>
-
-
-                <conditional name="optionLog">
-			<param name="log" type="select" label="calculate log option" help="use log on x- or y-axis (write 'x', 'y' or 'xy')">
-					<option value="Yes">Yes</option>
-					<option value="No" selected="true">No</option>
-			</param>
-			<when value="Yes">
-				<param name="logOnAxisLabel" type="text" value="y" label="use log on x- or y-axis (write 'x', 'y' or 'xy')"/>
-			</when>
-			<when value="No">
-			</when>
-		</conditional>
-                <param name="shape" type="text" value="barplot" label="shape of the plot [format: choice (barplot, line, points, heatPoints)]"/>
-	</inputs>
-	
-	<outputs>
-		<data name="outputFile" format="png" label="[plot] Output file"/>
-	</outputs>
-</tool>
--- a/SMART/galaxy/plotRepartition.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-<tool id="plotRepartition" name="plot repartition">
-	<description>Plot the repartition of different data on a whole genome. (This tool uses only 1 input file, the different values are stored in the tags. )</description>
-	<command interpreter="python">
-		../Java/Python/WrappPlotRepartition.py -i $inputFileName
-		-n $names
-		$normalize
-		#if $optionColor.Color == 'Yes':
-			-c $optionColor.colValue
-		#end if		
-		-f $format
-		
-		#if $optionLog.log == 'Yes':
-			-l $optionLog.logVal
-		#end if	
-		
-		-o $outputFilePNG
-	</command>
-
-	<inputs>
-		<param name="inputFileName" type="data" label="Input Gff3 File" format="gff3"/>
-		<param name="names" type="text" value="None" label="name for the tags (separated by commas and no space) [compulsory option]"/>
-		<param name="normalize" type="boolean" truevalue="-r" falsevalue="" checked="false" label="normalize data (when panels are different)"/>
-		<param name="format" type="text" value="png" label="format of the output file[default: png]"/>
-		
-		<conditional name="optionColor">
-			<param name="Color" type="select" label="scolor of the lines (separated by commas and no space) ">
-					<option value="Yes">Yes</option>
-					<option value="No" selected="true">No</option>
-			</param>
-			<when value="Yes">
-				<param name="colValue" type="text" value="None"/>
-			</when>
-			<when value="No">
-			</when>
-		</conditional>
-		
-		<conditional name="optionLog">
-			<param name="log" type="select" label="use log on x- or y-axis (write 'x', 'y' or 'xy')">
-					<option value="Yes">Yes</option>
-					<option value="No" selected="true">No</option>
-			</param>
-			<when value="Yes">
-				<param name="logVal" type="text" value=" "/>
-			</when>
-			<when value="No">
-			</when>
-		</conditional>	
-		
-	</inputs>
-
-	<outputs>
-		<data name="outputFilePNG" format="tar" label="[plotRepartition]out file"/>
-	</outputs> 
-	
-	<help>
-        This script gives a .tar out file, if you want to take look at the results, you have to download it.
-    </help>	
-	
-</tool>
--- a/SMART/galaxy/qualToFastq.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="qualToFastq" name="qual -> Fastq">
-  <description>Convert a file in FASTA/Qual format to FastQ format.</description>
-  <command interpreter="python"> ../Java/Python/qualToFastq.py -f $inputFastaFile -q $inputQualFile -o $outputFile </command>
-  <inputs>
-    <param name="inputFastaFile" type="data" label="Input fasta File" format="fasta"/>
-    <param name="inputQualFile" type="data" label="Input qual File" format="txt"/>
-  </inputs>
-
-  <outputs>
-    <data format="fastq" name="outputFile" label="[qual -> Fastq] Output File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
\ No newline at end of file
--- a/SMART/galaxy/restrictSequenceList.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-<tool id="restrictSequenceList" name="restrict sequence list">
-  <description>Keep the elements of a list of sequences whose name is mentionned in a given file.</description>
-  <command interpreter="python"> ../Java/Python/restrictSequenceList.py -i $inputFile -f fasta -n $name -o $outputFile </command>
-  
-  <inputs>
-	<param name="inputFile" type="data" label="Input fasta File" format="fasta"/>
-	<param name="name" type="data" label="The txt file contains the names of the transcripts." format="txt"/> 
-  </inputs>
-
-  <outputs>
-    <data format="fasta" name="outputFile" label="[restrictSequenceList] Output File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/testArgum.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-<tool id="test_argument" name="test_argu" version="1.0.0">
-  <description>To test the arguments from shell.</description>
-  <command> 
-../testArgu.sh $test_out 
-#for $i in $replicate_groups
-#for $j in $i.replicates
-$j.bam_alignment:#slurp
-#end for
-#end for
-    >> $Log_File </command>
-  <inputs>
-	<param format="gff3" name="anno_input_selected" type="data" label="Genome annotation in GFF3 file" help="A tab delimited format for storing sequence features and annotations"/>
-   <repeat name="replicate_groups" title="Replicate group" min="2">
-     <repeat name="replicates" title="Replicate">
-      <param format="fastq" name="bam_alignment" type="data" label="BAM alignment file" help="BAM alignment file. Can be generated from SAM files using the SAM Tools."/>
-     </repeat>
-   </repeat>
-  </inputs>
-
-  <outputs>
-    <data format="txt" name="test_out" label="DESeq result"/>
-	<data format="txt" name="Log_File" label="DESeq result"/>
-  </outputs>
-</tool>
--- a/SMART/galaxy/testR.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,19 +0,0 @@
-<tool id="testDiffExpAnal" name="Differential Expression Analysis">
-  <description>Differential expression analysis for sequence count data (DESeq)</description>
-  <command interpreter="sh"> ../DiffExpAnal/testR.sh $inputFile $columnsOfGeneName $columnsOfCondition1 $columnsOfCondition2 $outputFileCSV $outputFilePNG 2>$outputLog </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="tabular"/>
-	<param name="columnsOfGeneName" type="text" value="0" label="Please indicate the column numbers of gene names with ',' separator. If There are not gene names, default value is 0."/>
-	<param name="columnsOfCondition1" type="text" value="1,2" label="Please indicate the column numbers of condition1 with ',' separator."/>
-	<param name="columnsOfCondition2" type="text" value="3,4" label="Please indicate the column numbers of condition2 with ',' separator."/>
-  </inputs>
-
-  <outputs>
-    <data format="tabular" name="outputFileCSV" label="[DiffExpAnal] Output CSV File"/>
-	<data format="png" name="outputFilePNG" label="[DiffExpAnal] Output PNG File"/>
-    <data format="tabular" name="outputLog" label="[DiffExpAnal] Log File"/>
-  </outputs>
-
-  <help>
-  </help>
-</tool>
--- a/SMART/galaxy/trimAdaptor.xml	Mon Apr 22 11:08:07 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,47 +0,0 @@
-<tool id="trimAdaptor" name="trim adaptors">
-  <description>Remove the 3' adaptor of a list of reads.</description>
-  <command interpreter="python"> ../Java/Python/trimAdaptor.py -i $inputFile -f fastq
-  	-a $adaptor
-  	#if $OptionError.Error == "Yes":
-		-e $OptionError.ErrorVal
-	#end if	
-  	$noAdaptor $noAdaptorFile
-  	-o $outputFile  
-  </command>
-  
-  
-  <inputs>
-    <param name="inputFile" type="data" label="Input fastq File" format="fastq"/>
-	<param name="adaptor" type="text" value="None" label="adaptor [compulsory option]"/> 
-	<conditional name="OptionError">
-		<param name="Error" type="select" label="number of errors in percent">
-			<option value="Yes">Yes</option>
-			<option value="No" selected="true">No</option>
-		</param>
-		<when value="Yes">
-			<param name="ErrorVal" type="integer" value="0" />
-		</when>
-		<when value="No">
-		</when>
-	</conditional>	
-	<param name="noAdaptor" type="boolean" truevalue="-n" falsevalue="" checked="false" label="log option" help="file name where to print sequences with no adaptor"/>
-  </inputs>
-
-  <outputs>
-    <data format="fastq" name="outputFile" label="[trimAdaptor] Output File"/>
-	<data name="noAdaptorFile" format="fastq" label="[trimAdaptor] Log File">
-		<filter>noAdaptor</filter>
-	</data>
-  </outputs>
-  <tests>
-    <test>
-      <param name="inputFile" value="short_fastq.fastq" />
-      <param name="adaptor" value="AAAA" />
-      <param name ="Error" value="No"/>
-      <param name ="noAdaptor" value="False"/>
-      <output name="outputFile" file="exp_trimadaptator_short_fastq.fastq" />     
-    </test>
-  </tests>
-  <help>
-  </help>
-</tool>