Mercurial > repos > yufei-luo > s_mart
diff SMART/galaxy/test/CollapseReads.xml @ 6:769e306b7933
Change the repository level.
| author | yufei-luo |
|---|---|
| date | Fri, 18 Jan 2013 04:54:14 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/galaxy/test/CollapseReads.xml Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,49 @@ +<tool id="collapseReads" name="collapseReads"> + <description>Merges two reads if they have exactly the same genomic coordinates.</description> + <command interpreter="python"> + ../Java/Python/CollapseReads.py -i $formatType.inputFileName + #if $formatType.FormatInputFileName == 'bed': + -f bed + #elif $formatType.FormatInputFileName == 'gff': + -f gff + #elif $formatType.FormatInputFileName == 'gff2': + -f gff2 + #elif $formatType.FormatInputFileName == 'gff3': + -f gff3 + #end if + + -$strand + -o $outputFileGff + --galaxy + </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="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Strand option merges 2 different strands[default:False]."/> + </inputs> + + <outputs> + <data name="outputFileGff" format="gff3"/> + </outputs> + +</tool> \ No newline at end of file