Mercurial > repos > yufei-luo > s_mart
diff SMART/galaxy/changeTagName.xml @ 38:2c0c0a89fad7
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author | m-zytnicki |
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date | Thu, 02 May 2013 09:56:47 -0400 |
parents | |
children | 1236e5a49595 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/galaxy/changeTagName.xml Thu May 02 09:56:47 2013 -0400 @@ -0,0 +1,51 @@ +<tool id="changeTagName" name="change tag name"> + <description>Change the name of a tag in a GFF file.</description> + <requirements> + <requirement type="set_environment">PYTHONPATH</requirement> + </requirements> + <command interpreter="python"> + ../Java/Python/changeTagName.py -i $formatType.inputFileName + #elif $formatType.FormatInputFileName == 'gff': + -f gff + #elif $formatType.FormatInputFileName == 'gff2': + -f gff2 + #elif $formatType.FormatInputFileName == 'gff3': + -f gff3 + #end if + + -t $Tag + -n $name + + -o $outputFileGff + </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="Tag" type="text" label="tag option" help="The tag you want to change"/> + <param name="name" type="text" label="name option" help="A new name for the tag"/> + </inputs> + + <outputs> + <data name="outputFileGff" format="gff3" label="[change tag name] Output File"/> + </outputs> + + <help> + Change the name of a tag in the 9th field of a GFF3 file (please consult http://www.sequenceontology.org/gff3.shtml to know more about this format). + </help> +</tool>