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

Uploaded

--- a/SMART/galaxy/CleanTranscriptFile.xml	Fri Apr 19 10:13:11 2013 -0400
+++ b/SMART/galaxy/CleanTranscriptFile.xml	Mon Apr 22 11:08:07 2013 -0400
@@ -1,5 +1,5 @@
-<tool id="CleanTranscriptFile" name="Clean Transcript File">
-	<description> Clean a transcript file so that it is useable for S-MART.</description>
+<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
@@ -57,4 +57,17 @@
 		</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>