Galaxy |

Changeset 3:b41c88a53578 (2014-08-21)

Previous changeset 2:397067d90a77 (2014-08-21)

Commit message:
Uploaded

added:
submatch.pl
submatch.xml

diff -r 397067d90a77 -r b41c88a53578 submatch.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/submatch.pl Thu Aug 21 15:58:18 2014 -0400

[

@@ -0,0 +1,41 @@
+#!/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 397067d90a77 -r b41c88a53578 submatch.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/submatch.xml Thu Aug 21 15:58:18 2014 -0400

@@ -0,0 +1,49 @@
+
+<tool id="submatch" 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>