Mercurial > repos > yufei-luo > s_mart
diff SMART/galaxy/changeTagName.xml @ 31:0ab839023fe4
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 14:33:21 -0400 |
parents | 94ab73e8a190 |
children |
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--- a/SMART/galaxy/changeTagName.xml Mon Apr 29 03:45:52 2013 -0400 +++ b/SMART/galaxy/changeTagName.xml Tue Apr 30 14:33:21 2013 -0400 @@ -1,10 +1,9 @@ <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> + <description>Changes the name of tag of a list of transcripts.</description> <command interpreter="python"> ../Java/Python/changeTagName.py -i $formatType.inputFileName + #if $formatType.FormatInputFileName == 'bed': + -f bed #elif $formatType.FormatInputFileName == 'gff': -f gff #elif $formatType.FormatInputFileName == 'gff2': @@ -22,10 +21,14 @@ <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> @@ -37,15 +40,15 @@ </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"/> + <param name="Tag" type="text" value="None" label="tag option" help="A given tag, you must choose a tag."/> + <param name="name" type="text" value="None" label="name option" help="new name for the tag, you must choose a new name."/> + + + </inputs> <outputs> - <data name="outputFileGff" format="gff3" label="[change tag name] Output File"/> + <data name="outputFileGff" format="gff3" label="[changeTagName] 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>