Mercurial > repos > dsobral > flip_columns_on_condition

changeset 0:633ca40ded01

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Uploaded
author dsobral
date Thu, 15 Mar 2012 11:47:32 -0400
parents
children a0e05808610a
files reorient_coordinates.xml
diffstat 1 files changed, 46 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reorient_coordinates.xml	Thu Mar 15 11:47:32 2012 -0400
@@ -0,0 +1,46 @@
+<tool id="reorient_coordinates" name="Reorient Coordinates" version="0.1.0">
+  <description>Switches Start and End if needed</description>
+
+  <command interpreter="perl">reorient_coordinates.pl $input_file $output_file</command>
+  
+  <inputs>
+      <param name="input_file" type="data" format="tabular" label="3-column tabular file with columns 2 and 3 indicating genomic positions"/>             
+   </inputs>
+   
+  <outputs>
+    <data name="output_file" format="tabular" />
+  </outputs>
+       
+<!-- TODO implement tests: namely generate test data and put it in place     
+  	<tests>
+		<test>
+			<param name="input_file" value="test_transcript_count.bam" />
+			<param name="coherent" value="1" />
+			<output name="output_file" file="test_transcript_count.tab" />
+		</test>
+	</tests>        
+-->       
+    <help>
+    
+Switches positions in a tabular file to guarantee that the 2nd colum is always less or the same as the 3rd column.
+
+E.g.
+datafile:
+entry1	100	200
+entry2	200	200
+entry3	300	200
+
+Output:
+entry1	100	200
+entry2	200	200
+entry3	200	300
+
+------
+
+**Citation**
+
+This tools and Galaxy wrapper was developed by the IGC Bioinformatics unit (author: Daniel Sobral dsobral@igc.gulbenkian.pt)
+
+  </help>
+
+  </tool>
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