# HG changeset patch
# User m-zytnicki
# Date 1366380791 14400
# Node ID c79b9ae3f65fc30d2c04a42a16cbe6f9c5b436ca
# Parent  03045debed6e8490b7ca66905d228e6bcd5f069a
Deleted selected files

diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/ConvertTranscriptFile_BedToCsv.xml
--- a/SMART/galaxy/ConvertTranscriptFile_BedToCsv.xml	Wed Apr 17 10:39:35 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>
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/ConvertTranscriptFile_BedToGff2.xml
--- a/SMART/galaxy/ConvertTranscriptFile_BedToGff2.xml	Wed Apr 17 10:39:35 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>
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/ConvertTranscriptFile_BedToGff3.xml
--- a/SMART/galaxy/ConvertTranscriptFile_BedToGff3.xml	Wed Apr 17 10:39:35 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>
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/ConvertTranscriptFile_BedToSam.xml
--- a/SMART/galaxy/ConvertTranscriptFile_BedToSam.xml	Wed Apr 17 10:39:35 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>
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/ConvertTranscriptFile_BlastToCsv.xml
--- a/SMART/galaxy/ConvertTranscriptFile_BlastToCsv.xml	Wed Apr 17 10:39:35 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>
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/ConvertTranscriptFile_BlastToGff2.xml
--- a/SMART/galaxy/ConvertTranscriptFile_BlastToGff2.xml	Wed Apr 17 10:39:35 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>
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/ConvertTranscriptFile_BlastToGff3.xml
--- a/SMART/galaxy/ConvertTranscriptFile_BlastToGff3.xml	Wed Apr 17 10:39:35 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>
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/ConvertTranscriptFile_BlastToSam.xml
--- a/SMART/galaxy/ConvertTranscriptFile_BlastToSam.xml	Wed Apr 17 10:39:35 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>
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/ConvertTranscriptFile_FastqToFasta.xml
--- a/SMART/galaxy/ConvertTranscriptFile_FastqToFasta.xml	Wed Apr 17 10:39:35 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>
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/ConvertTranscriptFile_Gff2ToCsv.xml
--- a/SMART/galaxy/ConvertTranscriptFile_Gff2ToCsv.xml	Wed Apr 17 10:39:35 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>
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/ConvertTranscriptFile_Gff2ToGff3.xml
--- a/SMART/galaxy/ConvertTranscriptFile_Gff2ToGff3.xml	Wed Apr 17 10:39:35 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>
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/ConvertTranscriptFile_Gff2ToSam.xml
--- a/SMART/galaxy/ConvertTranscriptFile_Gff2ToSam.xml	Wed Apr 17 10:39:35 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>
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/ConvertTranscriptFile_Gff3ToCsv.xml
--- a/SMART/galaxy/ConvertTranscriptFile_Gff3ToCsv.xml	Wed Apr 17 10:39:35 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>
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/ConvertTranscriptFile_Gff3ToGff2.xml
--- a/SMART/galaxy/ConvertTranscriptFile_Gff3ToGff2.xml	Wed Apr 17 10:39:35 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>
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/ConvertTranscriptFile_Gff3ToSam.xml
--- a/SMART/galaxy/ConvertTranscriptFile_Gff3ToSam.xml	Wed Apr 17 10:39:35 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>
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/ConvertTranscriptFile_Gff3ToWig.xml
--- a/SMART/galaxy/ConvertTranscriptFile_Gff3ToWig.xml	Wed Apr 17 10:39:35 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
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/ConvertTranscriptFile_SamToCsv.xml
--- a/SMART/galaxy/ConvertTranscriptFile_SamToCsv.xml	Wed Apr 17 10:39:35 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>
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/ConvertTranscriptFile_SamToGff2.xml
--- a/SMART/galaxy/ConvertTranscriptFile_SamToGff2.xml	Wed Apr 17 10:39:35 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>
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/ConvertTranscriptFile_SamToGff3.xml
--- a/SMART/galaxy/ConvertTranscriptFile_SamToGff3.xml	Wed Apr 17 10:39:35 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>
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/testArgum.xml
--- a/SMART/galaxy/testArgum.xml	Wed Apr 17 10:39:35 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>
diff -r 03045debed6e -r c79b9ae3f65f SMART/galaxy/testR.xml
--- a/SMART/galaxy/testR.xml	Wed Apr 17 10:39:35 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>