Mercurial > repos > yufei-luo > s_mart
changeset 59:2a4884ba3e5c
Uploaded
| author | m-zytnicki |
|---|---|
| date | Mon, 10 Feb 2014 03:39:09 -0500 |
| parents | 5f5c9b74c2dd |
| children | 90f4b29d884f |
| files | SMART/galaxy/removeExonLines.xml SMART/galaxy/removeIntrons.xml |
| diffstat | 2 files changed, 24 insertions(+), 6 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/galaxy/removeExonLines.xml Mon Feb 10 03:39:09 2014 -0500 @@ -0,0 +1,18 @@ +<tool id="removeExonLines" name="remove exon lines"> + <description>Removes the introns of the transcript files.</description> + <requirements> + <requirement type="set_environment">PYTHONPATH</requirement> + </requirements> + <command interpreter="python"> ../Java/Python/RemoveExons.py -i $inputFile -f gff3 -o $outputFile </command> + <inputs> + <param name="inputFile" format="gff3" type="data" label="Input File"/> + </inputs> + + <outputs> + <data format="gff3" name="outputFile" label="[remove introns] output file"/> + </outputs> + + <help> + Simply remove the introns of the input file, thus getting the unmatured transcript. + </help> +</tool>
--- a/SMART/galaxy/removeIntrons.xml Fri Feb 07 11:53:36 2014 -0500 +++ b/SMART/galaxy/removeIntrons.xml Mon Feb 10 03:39:09 2014 -0500 @@ -15,22 +15,22 @@ <option value="gtf">gtf</option> </param> <when value="bed"> - <param name="inputFileName" format="bed" type="data" label="Input File 1"/> + <param name="inputFileName" format="bed" type="data" label="Input File"/> </when> <when value="gff"> - <param name="inputFileName" format="gff" type="data" label="Input File 1"/> + <param name="inputFileName" format="gff" type="data" label="Input File"/> </when> <when value="gff2"> - <param name="inputFileName" format="gff2" type="data" label="Input File 1"/> + <param name="inputFileName" format="gff2" type="data" label="Input File"/> </when> <when value="gff3"> - <param name="inputFileName" format="gff3" type="data" label="Input File 1"/> + <param name="inputFileName" format="gff3" type="data" label="Input File"/> </when> <when value="sam"> - <param name="inputFileName" format="sam" type="data" label="Input File 1"/> + <param name="inputFileName" format="sam" type="data" label="Input File"/> </when> <when value="gtf"> - <param name="inputFileName" format="gtf" type="data" label="Input File 1"/> + <param name="inputFileName" format="gtf" type="data" label="Input File"/> </when> </conditional> </inputs>