# HG changeset patch # User m-zytnicki # Date 1366643381 14400 # Node ID 6135c3075bc5c21b3d47ad6bc93bc91839cac8f6 # Parent 440ceca58672a32dbefc73f5bc29651f8b815be2 Deleted selected files diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/ConvertTranscriptFile_BedToCsv.xml --- 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 @@ - - Convert Bed File to Csv File. - ../Java/Python/convertTranscriptFile.py -i $inputFile -f bed -o $outputFile -g csv yes 2>$logFile - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/ConvertTranscriptFile_BedToGff2.xml --- 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 @@ - - Convert Bed File to Gff2 File. - ../Java/Python/convertTranscriptFile.py -i $inputFile -f bed -o $outputFile -g gff yes 2>$logFile - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/ConvertTranscriptFile_BedToGff3.xml --- 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 @@ - - Convert Bed File to Gff3 File. - ../Java/Python/convertTranscriptFile.py -i $inputFile -f bed -o $outputFile -g gff3 yes 2>$logFile - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/ConvertTranscriptFile_BedToSam.xml --- 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 @@ - - Convert Bed File to Sam File. - ../Java/Python/convertTranscriptFile.py -i $inputFile -f bed -o $outputFile -g sam yes 2>$logFile - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/ConvertTranscriptFile_BlastToCsv.xml --- 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 @@ - - Convert Blast (-m 8) File to Csv File. - ../Java/Python/convertTranscriptFile.py -i $inputFile -f blast -o $outputFile -g csv yes 2>$logFile - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/ConvertTranscriptFile_BlastToGff2.xml --- 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 @@ - - Convert Blast (-m 8) File to Gff2 File. - ../Java/Python/convertTranscriptFile.py -i $inputFile -f blast -o $outputFile -g gff2 yes 2>$logFile - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/ConvertTranscriptFile_BlastToGff3.xml --- 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 @@ - - Convert Blast (-m 8) File to Gff3 File. - ../Java/Python/convertTranscriptFile.py -i $inputFile -f blast -o $outputFile -g gff3 yes 2>$logFile - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/ConvertTranscriptFile_BlastToSam.xml --- 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 @@ - - Convert Blast (-m 8) File to Sam File. - ../Java/Python/convertTranscriptFile.py -i $inputFile -f blast -o $outputFile -g sam yes 2>$logFile - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/ConvertTranscriptFile_FastqToFasta.xml --- 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 @@ - - Convert Fastq File to Fasta File. - ../Java/Python/fastqToFasta.py -i $inputFile -o $outputFile 2>$logFile - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/ConvertTranscriptFile_Gff2ToCsv.xml --- 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 @@ - - Convert Gff2 File to Csv File. - ../Java/Python/convertTranscriptFile.py -i $inputFile -f gff2 -o $outputFile -g csv yes 2>$logFile - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/ConvertTranscriptFile_Gff2ToGff3.xml --- 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 @@ - - Convert Gff2 File to Gff3 File. - ../Java/Python/convertTranscriptFile.py -i $inputFile -f gff2 -o $outputFile -g gff3 yes 2>$logFile - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/ConvertTranscriptFile_Gff2ToSam.xml --- 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 @@ - - Convert Gff2 File to Sam File. - ../Java/Python/convertTranscriptFile.py -i $inputFile -f gff2 -o $outputFile -g sam yes 2>$logFile - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/ConvertTranscriptFile_Gff3ToCsv.xml --- 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 @@ - - Convert Gff3 File to Csv File. - ../Java/Python/convertTranscriptFile.py -i $inputFile -f gff3 -o $outputFile -g csv yes 2>$logFile - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/ConvertTranscriptFile_Gff3ToGff2.xml --- 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 @@ - - Convert Gff3 File to Gff2 File. - ../Java/Python/convertTranscriptFile.py -i $inputFile -f gff3 -o $outputFile -g gff2 yes 2>$logFile - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/ConvertTranscriptFile_Gff3ToSam.xml --- 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 @@ - - Convert Gff3 File to Sam File. - ../Java/Python/convertTranscriptFile.py -i $inputFile -f gff3 -o $outputFile -g sam yes 2>$logFile - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/ConvertTranscriptFile_Gff3ToWig.xml --- 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 @@ - - Convert Gff3 File to Wig File. - ../Java/Python/convertTranscriptFile.py -i $inputFile -f gff3 -o $outputFile -g wig yes 2>$logFile - - - - - - - - - - - - \ No newline at end of file diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/ConvertTranscriptFile_SamToCsv.xml --- 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 @@ - - Convert Sam File to Csv File. - ../Java/Python/convertTranscriptFile.py -i $inputFile -f sam -o $outputFile -g csv yes 2>$logFile - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/ConvertTranscriptFile_SamToGff2.xml --- 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 @@ - - Convert Sam File to Gff2 File. - ../Java/Python/convertTranscriptFile.py -i $inputFile -f sam -o $outputFile -g gff2 yes 2>$logFile - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/ConvertTranscriptFile_SamToGff3.xml --- 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 @@ - - Convert Sam File to Gff3 File. - ../Java/Python/convertTranscriptFile.py -i $inputFile -f sam -o $outputFile -g gff3 yes 2>$logFile - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/FindOverlaps_optim.xml --- 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 @@ - - Finds the overlapped reference reads. - - ../Java/Python/FindOverlaps_optim.py -i $inputRef -j $inputQ -o $outputFileGff - - - - - - - - - - - - \ No newline at end of file diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/findTss.xml --- 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 @@ - - Find the transcription start site of a list of transcripts. - - ../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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - excel - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/getNb.xml --- 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 @@ - - Get the distribution of exons per transcripts, or mapping per read, or transcript per cluster. - - ../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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/mappingToCoordinates.xml --- 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 @@ - - Converts a mapping type file(given by a mapping tool) to a GFF3 type file. - - ../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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/modifyFasta.xml --- 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 @@ - - Extend or shring a list of sequences. - ../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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/plot.xml --- 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 @@ - - Plot some information from a list of transcripts. - - ../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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/plotRepartition.xml --- 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 @@ - - 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. ) - - ../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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This script gives a .tar out file, if you want to take look at the results, you have to download it. - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/qualToFastq.xml --- 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 @@ - - Convert a file in FASTA/Qual format to FastQ format. - ../Java/Python/qualToFastq.py -f $inputFastaFile -q $inputQualFile -o $outputFile - - - - - - - - - - - - \ No newline at end of file diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/restrictSequenceList.xml --- 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 @@ - - Keep the elements of a list of sequences whose name is mentionned in a given file. - ../Java/Python/restrictSequenceList.py -i $inputFile -f fasta -n $name -o $outputFile - - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/testArgum.xml --- 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 @@ - - To test the arguments from shell. - -../testArgu.sh $test_out -#for $i in $replicate_groups -#for $j in $i.replicates -$j.bam_alignment:#slurp -#end for -#end for - >> $Log_File - - - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/testR.xml --- 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 @@ - - Differential expression analysis for sequence count data (DESeq) - ../DiffExpAnal/testR.sh $inputFile $columnsOfGeneName $columnsOfCondition1 $columnsOfCondition2 $outputFileCSV $outputFilePNG 2>$outputLog - - - - - - - - - - - - - - - - diff -r 440ceca58672 -r 6135c3075bc5 SMART/galaxy/trimAdaptor.xml --- 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 @@ - - Remove the 3' adaptor of a list of reads. - ../Java/Python/trimAdaptor.py -i $inputFile -f fastq - -a $adaptor - #if $OptionError.Error == "Yes": - -e $OptionError.ErrorVal - #end if - $noAdaptor $noAdaptorFile - -o $outputFile - - - - - - - - - - - - - - - - - - - - - - - - noAdaptor - - - - - - - - - - - - - -