Mercurial > repos > yufei-luo > s_mart
changeset 14:c79b9ae3f65f
Deleted selected files
| author | m-zytnicki |
|---|---|
| date | Fri, 19 Apr 2013 10:13:11 -0400 |
| parents | 03045debed6e |
| children | 440ceca58672 |
| 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/testArgum.xml SMART/galaxy/testR.xml |
| diffstat | 21 files changed, 0 insertions(+), 328 deletions(-) [+] |
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--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>