comparison SMART/galaxy/CleanTranscriptFile.xml @ 15:440ceca58672

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14:c79b9ae3f65f

<tool id="CleanTranscriptFile" name="Clean Transcript File">
	<description> Clean a transcript file so that it is useable for S-MART.</description>
	<command interpreter="python"> ../Java/Python/CleanTranscriptFile.py -i $formatType.inputFileName 
		#if $formatType.FormatInputFileName == 'gff':
		 	-f gff
		#elif $formatType.FormatInputFileName == 'gtf':
			-f gtf

			<when input="formatType.FormatInputFileName" value="gff3" format="gff3" />
		</change_format> 
		</data>

	</outputs>
</tool>

15:440ceca58672

<tool id="CleanTranscriptFile" name="clean Transcript File">
	<description>Clean a transcript file so that it is useable for S-MART.</description>
	<command interpreter="python"> ../Java/Python/CleanTranscriptFile.py -i $formatType.inputFileName 
		#if $formatType.FormatInputFileName == 'gff':
		 	-f gff
		#elif $formatType.FormatInputFileName == 'gtf':
			-f gtf

			<when input="formatType.FormatInputFileName" value="gff3" format="gff3" />
		</change_format> 
		</data>

	</outputs>
<tests>
    <test>
      <param name="FormatInputFileName" value="gtf" />
      <param name="inputFileName" value="genes.gtf" />
      <param name="type" value="No" />
      <output name="outputFile" file="exp_cleantranscriptfile_genes.gtf" />
    </test>
  </tests>

	<help>
		A GFF/GTF file (please consult http://www.sequenceontology.org/gff3.shtml to know more about the GFF3 format, and http://mblab.wustl.edu/GTF22.html for the GTF format) may contain different sources of information: chromosome size, genes, transcripts, etc. S-MART mostly works on transcripts. This scripts filters the input file to keep the information you really want, based on the feature (3rd column).
	</help>

</tool>