From 61aa1fe894646f8a2e0d041e7f45a13ba58c2047 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Fri, 25 Apr 2008 19:05:56 +0000
Subject: [PATCH] Fix for EMBOSS 5 cpgplot tool.

---
 tools/emboss_5/emboss_cpgplot.xml        | 28 ++++++++----------------
 tools/emboss_5/emboss_cpgplot_wrapper.pl |  2 +-
 2 files changed, 10 insertions(+), 20 deletions(-)

diff --git a/tools/emboss_5/emboss_cpgplot.xml b/tools/emboss_5/emboss_cpgplot.xml
index d7b2104a760..04ddb12c208 100644
--- a/tools/emboss_5/emboss_cpgplot.xml
+++ b/tools/emboss_5/emboss_cpgplot.xml
@@ -1,42 +1,32 @@
 <tool id="EMBOSS: cpgplot15" name="cpgplot" version="5.0.0">
   <description>Plot CpG rich areas</description>
-  <command interpreter="perl">emboss_cpgplot_wrapper.pl cpgplot -sequence $input1 -window $window -minlen $minlen -minpc $minpc -outfile $out_file1 -graph png -goutfile3 $out_file2
-  -outfeat $out_file3 -offormat4 $out_format3 -minoe $minoe -auto</command>
+  <command interpreter="perl">emboss_cpgplot_wrapper.pl /home/universe/linux-i686/EMBOSS-5.0.0/bin/cpgplot -sequence $input1 -window $window -minlen $minlen -minpc $minpc -outfile $outfile -graph png -goutfile $goutfile -outfeat $outfeat -minoe $minoe -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>On query</label>
     </param>
-    <param name="window" size="4" type="text" value="100">
+    <param name="window" size="4" type="integer" value="100">
       <label>Window Size</label>
     </param>
-    <!--  <param name="shift" size="4" type="text" value="1">
-      <label>Step size (shift)</label> 
-    </param> -->
-    <param name="minlen" size="4" type="text" value="200">
+    <param name="minlen" size="4" type="integer" value="200">
       <label>Minimum length</label>
     </param>
-    <param name="minoe" size="4" type="text" value="0.6">
+    <param name="minoe" size="4" type="float" value="0.6">
       <label>Minimum average observed to expected ratio</label>
     </param>
-    <param name="minpc" size="4" type="text" value="50.0">
+    <param name="minpc" size="4" type="float" value="50.0">
       <label>Minimum average percentage of G plus C</label>
     </param>
-    <param name="out_format3" type="select">
-      <label>Output Feature File Format</label>
-      <option value="gff">GFF</option>
-      <option value="embl">EMBL</option>
-      <option value="swiss">SwissProt</option>
-    </param>
   </inputs>
   <outputs>
-    <data format="txt" name="out_file1" />
-    <data format="png" name="out_file2" />
-    <data format="gff" name="out_file3" />
+    <data format="cpgplot" name="outfile" />
+    <data format="png" name="goutfile" />
+    <data format="gff" name="outfeat" />
   </outputs>
   <code file="emboss_format_corrector.py" />
   <help>
     You can view the original documentation here_.
     
-    .. _here: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/cpgplot.html
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgplot.html
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_cpgplot_wrapper.pl b/tools/emboss_5/emboss_cpgplot_wrapper.pl
index 6d15d72ed37..6edbbbfd456 100644
--- a/tools/emboss_5/emboss_cpgplot_wrapper.pl
+++ b/tools/emboss_5/emboss_cpgplot_wrapper.pl
@@ -5,5 +5,5 @@ use File::Copy;
 my $cmd_string = join (" ",@ARGV);
 my $results = `$cmd_string`;
 my @files = split("\n",$results);
-my $fileNameOut = $ARGV[16];
+my $fileNameOut = $ARGV[14];
 move($fileNameOut.".1.png",$fileNameOut);