diff --git a/tools/emboss_5/emboss_coderet.xml b/tools/emboss_5/emboss_coderet.xml
new file mode 100644
index 00000000000..5a5f6f960d6
--- /dev/null
+++ b/tools/emboss_5/emboss_coderet.xml
@@ -0,0 +1,70 @@
+<tool id="EMBOSS_coderet13" name="coderet">
+  <description>Extract CDS, mRNA and translations from feature tables</description>
+  <!--  <command>coderet -seqall $input1 -outfile $out_file1 -osformat2 $out_format1 -cds $cds -mrna $mrna -translation $translation -auto</command>-->
+  <command>coderet -seqall $input1 -outfile $out_file1 -auto</command>
+  <inputs>
+    <param format="data" name="input1" type="data">
+      <label>On query</label>
+    </param>
+<!--    <param name="cds" type="boolean" truevalue="yes" falsevalue="no" checked="true">
+      <label>Extract CDS sequences</label>
+    </param>
+    <param name="mrna" type="select">
+      <label>Extract mRNA sequences</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="translation" type="select">
+      <label>Extract translated sequences</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param> 
+    <param name="out_format1" type="select">
+      <label>Output Sequence File Format</label>
+      <option value="fasta">FASTA (m)</option>
+      <option value="acedb">ACeDB (m)</option>
+      <option value="asn1">ASN.1 (m)</option>
+      <option value="clustal">Clustal (m)</option>
+      <option value="codata">CODATA (m)</option>
+      <option value="embl">EMBL (m)</option>
+      <option value="fitch">Fitch (m)</option>
+      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
+      <option value="genbank">GENBANK (m)</option>
+      <option value="gff">GFF (m)</option>
+      <option value="hennig86">Hennig86 (m)</option>
+      <option value="ig">Intelligenetics (m)</option>
+      <option value="jackknifer">Jackknifer (m)</option>
+      <option value="jackknifernon">Jackknifernon (m)</option>
+      <option value="mega">Mega (m)</option>
+      <option value="meganon">Meganon (m)</option>
+      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
+      <option value="pir">NBRF (PIR) (m)</option>
+      <option value="ncbi">NCBI style FASTA (m)</option>
+      <option value="nexus">Nexus/PAUP (m)</option>
+      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
+      <option value="phylip">PHYLIP interleaved (m)</option>
+      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
+      <option value="selex">SELEX (m)</option>
+      <option value="staden">Staden (s)</option>
+      <option value="strider">DNA strider (m)</option>
+      <option value="swiss">SwisProt entry (m)</option>
+      <option value="text">Plain sequence (s)</option>
+      <option value="treecon">Treecon (m)</option> 
+    </param> -->
+  </inputs>
+  <outputs>
+    <data format="coderet" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <output name="out_file1" file="emboss_coderet_out.coderet"/>
+    </test>
+  </tests>
+  <code file="emboss_format_corrector.py" />
+  <help>
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/coderet.html
+  </help>
+</tool>
diff --git a/tools/emboss_5/emboss_cpgplot.xml b/tools/emboss_5/emboss_cpgplot.xml
new file mode 100644
index 00000000000..f772bf29dab
--- /dev/null
+++ b/tools/emboss_5/emboss_cpgplot.xml
@@ -0,0 +1,42 @@
+<tool id="EMBOSS_cpgplot15" name="cpgplot">
+  <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>
+  <inputs>
+    <param format="data" name="input1" type="data">
+      <label>On query</label>
+    </param>
+    <param name="window" size="4" type="text" 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">
+      <label>Minimum length</label>
+    </param>
+    <param name="minoe" size="4" type="text" value="0.6">
+      <label>Minimum average observed to expected ratio</label>
+    </param>
+    <param name="minpc" size="4" type="text" 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" />
+  </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
+  </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
new file mode 100644
index 00000000000..6d15d72ed37
--- /dev/null
+++ b/tools/emboss_5/emboss_cpgplot_wrapper.pl
@@ -0,0 +1,9 @@
+#! /usr/bin/perl -w
+use strict;
+use File::Copy;
+
+my $cmd_string = join (" ",@ARGV);
+my $results = `$cmd_string`;
+my @files = split("\n",$results);
+my $fileNameOut = $ARGV[16];
+move($fileNameOut.".1.png",$fileNameOut);
diff --git a/tools/emboss_5/emboss_diffseq.xml b/tools/emboss_5/emboss_diffseq.xml
new file mode 100644
index 00000000000..6075b7bea8c
--- /dev/null
+++ b/tools/emboss_5/emboss_diffseq.xml
@@ -0,0 +1,63 @@
+<tool id="EMBOSS_diffseq22" name="diffseq">
+  <description>Find differences between nearly identical sequences</description>
+  <command>diffseq -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize $wordsize -globaldifferences $globaldifferences -rformat3
+  $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto</command>
+  <inputs>
+    <param format="data" name="input1" type="data">
+      <label>Sequence 1</label>
+    </param>
+    <param format="data" name="input2" type="data">
+      <label>Sequence 2</label>
+    </param>
+    <param name="wordsize" size="4" type="text" value="20">
+      <label>Wordsize</label>
+    </param>
+    <param name="globaldifferences" type="select">
+      <label>Report differences at the ends</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="out_format1" type="select">
+      <label>Output Report File Format</label>
+      <option value="diffseq">Diffseq</option>
+      <option value="embl">EMBL</option>
+      <option value="genbank">GENBANK</option>
+      <option value="gff">GFF</option>
+      <option value="pir">PIR</option>
+      <option value="swiss">SwissProt</option>
+      <option value="dbmotif">DbMotif</option>
+      <option value="excel">Excel (tab delimited)</option>
+      <option value="feattable">FeatTable</option>
+      <option value="motif">Motif</option>
+      <option value="regions">Regions</option>
+      <option value="seqtable">SeqTable</option>
+      <option value="simple">SRS Simple</option>
+      <option value="srs">SRS</option>
+      <option value="table">Table</option>
+      <option value="tagseq">TagSeq</option>
+    </param>
+    <param name="out_format2" type="select">
+      <label>Sequence 1 Output Feature File Format</label>
+      <option value="gff">GFF</option>
+      <option value="embl">EMBL</option>
+      <option value="swiss">SwissProt</option>
+    </param>
+    <param name="out_format3" type="select">
+      <label>Sequence 2 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="diffseq" name="out_file1" />
+    <data format="gff" name="out_file2" />
+    <data format="gff" name="out_file3" />
+  </outputs>
+  <code file="emboss_format_corrector.py" />
+  <help>
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/diffseq.html
+  </help>
+</tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_digest.xml b/tools/emboss_5/emboss_digest.xml
new file mode 100644
index 00000000000..1fb3e638519
--- /dev/null
+++ b/tools/emboss_5/emboss_digest.xml
@@ -0,0 +1,64 @@
+<tool id="EMBOSS_digest23" name="digest">
+  <description>Protein proteolytic enzyme or reagent cleavage digest</description>
+  <command>digest -sequence $input1 -outfile $out_file1 -menu $menu -unfavoured $unfavoured -overlap $overlap -allpartials $allpartials -rformat2 $out_format1 -auto</command>
+  <inputs>
+    <param format="data" name="input1" type="data">
+      <label>Sequence</label>
+    </param>
+    <param name="menu" type="select">
+      <label>Enzyme/Reagent</label>
+      <option value="1">Trypsin</option>
+      <option value="2">Lys-C</option>
+      <option value="3">Arg-C</option>
+      <option value="4">Asp-N</option>
+      <option value="5">V8-bicarb</option>
+      <option value="6">V8-phosph</option>
+      <option value="7">Chymotrypsin</option>
+      <option value="8">CNBr</option>
+    </param>
+    <param name="unfavoured" type="select">
+      <label>Trypsin will not normally cut after a K if it is followed by (e.g.) another K or a P. Specifying this shows those cuts, as well as the favoured ones.</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="overlap" type="select">
+      <label>Used for partial digestion. Shows all cuts from favoured cut sites plus 1..3, 2..4, 3..5 etc but not (e.g.) 2..5. Overlaps are therefore fragments with exactly one potential cut site
+      within it.</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="allpartials" type="select">
+      <label>As for overlap but fragments containing more than one potential cut site are included.</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="out_format1" type="select">
+      <label>Output Report File Format</label>
+      <option value="seqtable">SeqTable</option>
+      <option value="embl">EMBL</option>
+      <option value="genbank">GENBANK</option>
+      <option value="gff">GFF</option>
+      <option value="pir">PIR</option>
+      <option value="swiss">SwissProt</option>
+      <option value="dbmotif">DbMotif</option>
+      <option value="diffseq">Diffseq</option>
+      <option value="excel">Excel (tab delimited)</option>
+      <option value="feattable">FeatTable</option>
+      <option value="motif">Motif</option>
+      <option value="regions">Regions</option>
+      <option value="simple">SRS Simple</option>
+      <option value="srs">SRS</option>
+      <option value="table">Table</option>
+      <option value="tagseq">TagSeq</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="digest" name="out_file1" />
+  </outputs>
+  <code file="emboss_format_corrector.py" />
+  <help>
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/digest.html
+  </help>
+</tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_dotmatcher.xml b/tools/emboss_5/emboss_dotmatcher.xml
new file mode 100644
index 00000000000..183c69239b3
--- /dev/null
+++ b/tools/emboss_5/emboss_dotmatcher.xml
@@ -0,0 +1,28 @@
+<tool id="EMBOSS_dotmatcher24" name="dotmatcher">
+  <description>Displays a thresholded dotplot of two sequences</description>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl dotmatcher -asequence $input1 -bsequence $input2 -goutfile $out_file1 -windowsize $windowsize -threshold $threshold -graph png -xygraph png
+  -auto</command>
+  <inputs>
+    <param format="data" name="input1" type="data">
+      <label>Sequence 1</label>
+    </param>
+    <param format="data" name="input2" type="data">
+      <label>Sequence 2</label>
+    </param>
+    <param name="windowsize" size="4" type="text" value="10">
+      <label>Window size</label>
+    </param>
+    <param name="threshold" size="4" type="text" value="23">
+      <label>Threshold</label>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="png" name="out_file1" />
+  </outputs>
+  <!-- functional tests not possible since image output contains file name information and timestamp -->
+  <help>
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dotmatcher.html
+  </help>
+</tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_dotpath.xml b/tools/emboss_5/emboss_dotpath.xml
new file mode 100644
index 00000000000..bca25c0d7b6
--- /dev/null
+++ b/tools/emboss_5/emboss_dotpath.xml
@@ -0,0 +1,35 @@
+<tool id="EMBOSS: dotpath25" name="dotpath">
+  <description>Non-overlapping wordmatch dotplot of two sequences</description>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl dotpath -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -overlaps $overlaps -boxit $boxit -graph png
+  -auto</command>
+  <inputs>
+    <param format="data" name="input1" type="data">
+      <label>Sequence 1</label>
+    </param>
+    <param format="data" name="input2" type="data">
+      <label>Sequence 2</label>
+    </param>
+    <param name="wordsize" size="4" type="text" value="4">
+      <label>Word size (Integer 2 or more)</label>
+    </param>
+    <param name="overlaps" type="select">
+      <label>Display the overlapping matches (in red) as well as the minimal set of non-overlapping matches</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="boxit" type="select">
+      <label>Draw a box around dotplot</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="png" name="out_file1" />
+  </outputs>
+  <!-- functional tests not possible since image output contains file name information and timestamp -->
+  <help>
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dotpath.html
+  </help>
+</tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_dottup.xml b/tools/emboss_5/emboss_dottup.xml
new file mode 100644
index 00000000000..a57c5d472b8
--- /dev/null
+++ b/tools/emboss_5/emboss_dottup.xml
@@ -0,0 +1,29 @@
+<tool id="EMBOSS_dottup26" name="dottup">
+  <description>Displays a wordmatch dotplot of two sequences</description>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl dottup -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -boxit $boxit -graph png  -xygraph png -auto</command>
+  <inputs>
+    <param format="data" name="input1" type="data">
+      <label>Sequence 1</label>
+    </param>
+    <param format="data" name="input2" type="data">
+      <label>Sequence 2</label>
+    </param>
+    <param name="wordsize" size="4" type="text" value="4">
+      <label>Word size</label>
+    </param>
+    <param name="boxit" type="select">
+      <label>Draw a box around dotplot</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="png" name="out_file1" />
+  </outputs>
+  <!-- functional tests not possible since image output contains file name information and timestamp -->
+  <help>
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dottup.html
+  </help>
+</tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_dreg.xml b/tools/emboss_5/emboss_dreg.xml
new file mode 100644
index 00000000000..57a6a49bc2c
--- /dev/null
+++ b/tools/emboss_5/emboss_dreg.xml
@@ -0,0 +1,21 @@
+<tool id="EMBOSS_dreg27" name="dreg">
+  <description>Regular expression search of a nucleotide sequence</description>
+  <command>dreg -sequence $input1 -outfile $out_file1 -pattern "$pattern" -raccshow3 "no" -rusashow3 "no" -rdesshow3 "no" -auto</command>
+  <inputs>
+    <param format="data" name="input1" type="data">
+      <label>Sequence 1</label>
+    </param>
+    <param name="pattern" size="50" type="text" value="(AUG)">
+      <label>Regular expression pattern</label>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="dreg" name="out_file1" />
+  </outputs>
+  <!-- tests not possible since dreg timestamps output file -->  
+  <help>
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dreg.html
+  </help>
+</tool>
\ No newline at end of file