diff sort_chromosomal_position.xml @ 0:e77c9484b2d0 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sort_chromosomal_position.xml	Thu Oct 22 09:18:30 2015 -0400
@@ -0,0 +1,31 @@
+<tool id="sort_chrom_pos" name="Sort Chromosomal Position" version="1" >
+	<description> sort file by chromosome, then by position </description>
+	<command interpreter="bash">
+		sort_chromosomal_position.sh $infile $chrcol $startcol $endcol $num_headerlines $sorted_file
+	</command>
+	
+	
+	<inputs>
+										
+		<param name="infile" 	  type="data" 			label="select file to be sorted" help="must be a tab-separated file with a 1 line header"/>
+		<param name="chrcol"   type="data_column"    data_ref="infile" multiple="False" label="Chromosome Column" /> 
+		<param name="startcol" type="data_column"    data_ref="infile" multiple="False" label="Start Column"  /> 		
+		<param name="endcol"   type="data_column"    data_ref="infile" multiple="False" label="End Column"  /> 
+		<param name="num_headerlines" type="text" value="1" label="number of headerlines in your file" help="these lines will not be sorted"/>		
+	
+		<param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>		
+	</inputs>
+
+  <outputs>
+      <data format="tabular" name="sorted_file"  label="$fname ${tool.name} Annotated region on file ${on_string}"/>	 	
+     
+  </outputs>
+
+	<help> 
+
+ 
+</help>
+
+</tool>
+
+