# HG changeset patch
# User alan-blakely
# Date 1408651063 14400
# Node ID 397067d90a7782286762cac77a8cb574862c68d2
# Parent  9af08aa008de327004829d8b159317d75744f0a1
Deleted selected files

diff -r 9af08aa008de -r 397067d90a77 submatch/submatch.pl
--- a/submatch/submatch.pl	Thu Aug 21 12:52:21 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,41 +0,0 @@
-#!/usr/bin/perl -w                 
-use strict;
-my (@seq, @rep, $i, $n, $l, $t);
-
-open (SEQ, "<$ARGV[0]");
-open (REP, "<$ARGV[1]");
-open (OUT, ">$ARGV[2]");
-
-
-$i=$n=$l=0;
-
-
-
-while (<SEQ>){
-	chomp();
-	$seq[$i] = $_;
-	$i++;
-}
-while (<REP>){
-	$rep[$n] = $_;
-	$n++;
-
-}
-while ($l < $i){
-	$t=0;
-	while ($t < $n){
-		print OUT $rep[$t] if $rep[$t] =~ /$seq[$l]/;
-		$t++;
-	}
-	$l++;
-}
-
-
-
-close (SEQ);
-close (REP);
-close (OUT);
-
-#optional: remove duplicate lines using server-side shell command
-system("sort", "-u", "-o", "$ARGV[2]", "$ARGV[2]"); 
-    
diff -r 9af08aa008de -r 397067d90a77 submatch/submatch.xml
--- a/submatch/submatch.xml	Thu Aug 21 12:52:21 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-
-<tool id="pmatch" name="Filter by Substring Match">
-
-    <description>This tool allows for partial sequences to match lines containing a larger, more complete sequence. </description>
-
-    <command interpreter="perl">submatch.pl $sequences $report $output </command>
-
-    <inputs>
-
-	<param format="tabular" name="sequences" type="data" label="Tabular file containing list to filter on."/>
-	<param format="tabular" name="report" type="data" label="Tabular file to be filtered."/>
-
-    </inputs>
-
-    <outputs>
-        <data format="tabular" name="output" />
-    </outputs>
-  <tests>
-    <test>
-      <param name="sequences" value="submatch_input.tab"/>
-      <param name="report" value="submatch_input2.tab"/>
-      <output name="output" file="submatch_output.tab"/>
-    </test>
-  </tests>
-
-<help>
-
-
-
-Each line from the list file is converted to a regular expression of the form .*LINE.* 
-
-
-
-Lines from the second file that match the expression are returned. 
-
-
-
-
-This tool allows for partial sequences to match lines containing a larger more complete sequence. 
-
-Example: a file containing fragment amino acid sequences is used to select corresponding lines from a peptide report.  
-
-
-
-
-
-</help>
-
-</tool>