Mercurial > repos > yufei-luo > s_mart
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>