diff filter_columns.xml @ 0:e77c9484b2d0 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_columns.xml	Thu Oct 22 09:18:30 2015 -0400
@@ -0,0 +1,53 @@
+ <tool id="filter_columns" name="Filter Columns" version="1.2">
+
+  <description> filter file based on column values </description>
+  
+  <command interpreter="bash"> 
+  	filter_columns.sh 
+  		--infile $infile
+  		#for $f in $filters <!--get each var/mastervar file-->
+			--filter ${f.column},${f.condition},${f.value}
+		#end for
+		--outfile_rem $outputfile_removed
+		--outfile_ret $outputfile_retained		
+  </command>
+
+  <outputs>
+	  <data format="input" name="outputfile_removed"  label="${sample} - Removed lines Column filter on ${on_string}" metadata_source="infile"/>
+	  <data format="input" name="outputfile_retained" label="${sample} - Retained lines Column filter on ${on_string}" metadata_source="infile"/>
+  </outputs>
+  
+  <inputs>
+
+	<param name="infile" type="data" label="Select input file" help="expects header lines to be indicated by # or > symbols. First line is always considered header line"/>
+  	
+  	<repeat name="filters" title="Filter" min="1" help="Multiple filters: lines removed if match any of the filters, not all (rules are OR'd, not AND'd)">
+		<param name="column"    type="data_column"   data_ref="infile" multiple="False" label="Select Column to filter on"  /> 
+		<param name="condition" type="select" label="Remove line if column value.." help="you will receive both file with retained lines and file with removed lines">
+			<option value="nonempty">  	non-empty					</option>
+			<option value="empty"	>	empty						</option>
+			<option value="equals"	>	equals (string or number)	</option>
+			<option value="nequals"	>	not equals (string or number)</option>
+			<option value="contains"> 	contains (substring) 		</option>
+			<option value="ncontains"> 	does not contain (substring) </option>
+			<option value="gt"		>	greater than				</option>
+			<option value="ge"		>	greater than or equals		</option>
+			<option value="lt"		>	less than					</option>
+			<option value="le"		>	less than or equals			</option>
+		</param>
+		
+		
+		<param name="value" type="text" value="" label="enter number or string unless above option was set to empty or nonempty"/>		
+	</repeat>				
+  	 
+  	<param name="sample"	type="text" value="" label="Output File Name" help="Optional."/>	
+
+  </inputs>
+
+  <help>
+  
+**What it does**
+Concatenates 2 files
+
+  </help>
+</tool>