Mercurial > repos > yufei-luo > s_mart
diff smart_toolShed/SMART/galaxy/modifyGenomicCoordinates.xml @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
| author | yufei-luo |
|---|---|
| date | Thu, 17 Jan 2013 10:52:14 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/smart_toolShed/SMART/galaxy/modifyGenomicCoordinates.xml Thu Jan 17 10:52:14 2013 -0500 @@ -0,0 +1,126 @@ +<tool id="modifyGenomicCoordinates" name="modify genomic coordinates"> + <description>Extend or shrink a list of genomic coordinates.</description> + <command interpreter="python"> ../Java/Python/modifyGenomicCoordinates.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 + + #if $OptionStart.start == "Yes": + -s $OptionStart.startValue + #end if + + #if $OptionEnd.end == "Yes": + -e $OptionEnd.endValue + #end if + + #if $OptionFivePrim.five == "Yes": + -5 $OptionFivePrim.fivePValue + #end if + + #if $OptionTroisP.TroisP == "Yes": + -3 $OptionTroisP.ThreePValue + #end if + + -o $outputFile + </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> + + <conditional name="OptionStart"> + <param name="start" type="select" label="restrict to the start of the transcript"> + <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="restrict to the end of the transcript"> + <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> + + + <conditional name="OptionFivePrim"> + <param name="five" type="select" label="extend to the 5' direction"> + <option value="Yes">Yes</option> + <option value="No" selected="true">No</option> + </param> + <when value="Yes"> + <param name="fivePValue" type="integer" value="0"/> + </when> + <when value="No"> + </when> + </conditional> + + <conditional name="OptionTroisP"> + <param name="TroisP" type="select" label="extend to the 3' direction"> + <option value="Yes">Yes</option> + <option value="No" selected="true">No</option> + </param> + <when value="Yes"> + <param name="ThreePValue" type="integer" value="0"/> + </when> + <when value="No"> + </when> + </conditional> + + + </inputs> + + <outputs> + <data format="gff3" name="outputFile" label="[modifyGenomicCoordinates] Output File"/> + </outputs> + + <help> + </help> +</tool>