diff --git a/tools/emboss_5/emboss_equicktandem.xml b/tools/emboss_5/emboss_equicktandem.xml
new file mode 100644
index 00000000000..b9ef8eb231d
--- /dev/null
+++ b/tools/emboss_5/emboss_equicktandem.xml
@@ -0,0 +1,59 @@
+<tool id="EMBOSS_equicktandem31" name="equicktandem">
+  <description>Finds tandem repeats</description>
+  <command>equicktandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -maxrepeat $maxrepeat -threshold $threshold -rformat2 $out_format1 -auto</command>
+  <inputs>
+    <param format="fasta" name="input1" type="data">
+      <label>Sequence</label>
+    </param>
+    <param name="maxrepeat" size="4" type="text" value="600">
+      <label>Maximum repeat size</label>
+    </param>
+    <param name="threshold" size="4" type="text" value="20">
+      <label>Threshold score</label>
+    </param>
+    <param name="out_format1" type="select">
+      <label>Output Report File Format</label>
+      <option value="table">Table</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="seqtable">SeqTable</option>
+      <option value="simple">SRS Simple</option>
+      <option value="srs">SRS</option>
+      <option value="tagseq">TagSeq</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="table" name="out_file1" />
+    <data format="equicktandem" name="ofile2" />
+  </outputs>
+    <tests>
+    <test>
+      <param name="input1" value="1.fasta"/>
+      <param name="maxrepeat" value="600"/>
+      <param name="threshold" value="20"/>
+      <param name="out_format1" value="table"/>
+      <output name="ofile2" file="emboss_equicktandem_out.equicktandem"/>
+    </test>
+  </tests>
+  <code file="emboss_format_corrector.py" />
+  <help>
+.. class:: warningmark
+
+The input dataset needs to be sequences.
+
+-----
+
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/equicktandem.html
+  </help>
+</tool>
diff --git a/tools/emboss_5/emboss_etandem.xml b/tools/emboss_5/emboss_etandem.xml
new file mode 100644
index 00000000000..e5209f92fbe
--- /dev/null
+++ b/tools/emboss_5/emboss_etandem.xml
@@ -0,0 +1,77 @@
+<tool id="EMBOSS_etandem33" name="etandem">
+  <description>Looks for tandem repeats in a nucleotide sequence</description>
+  <command>etandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -minrepeat $minrepeat -maxrepeat $maxrepeat -threshold $threshold -mismatch $mismatch -uniform $uniform -rformat2 $out_format1 -auto</command>
+  <inputs>
+    <param format="fasta" name="input1" type="data">
+      <label>Sequence</label>
+    </param>
+    <param name="minrepeat" size="4" type="text" value="10">
+      <label>Minimum repeat size</label>
+    </param>
+    <param name="maxrepeat" size="4" type="text" value="10">
+      <label>Maximum repeat size</label>
+    </param>
+    <param name="threshold" size="4" type="text" value="20">
+      <label>Threshold score</label>
+    </param>
+    <param name="mismatch" type="select">
+      <label>Allow N as a mismatch</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="uniform" type="select">
+      <label>Allow uniform consensus</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="table">Table</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="seqtable">SeqTable</option>
+      <option value="simple">SRS Simple</option>
+      <option value="srs">SRS</option>
+      <option value="tagseq">TagSeq</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="etandem" name="out_file1" />
+    <data format="table" name="ofile2" />    
+  </outputs>
+    <tests>
+    <test>
+      <param name="input1" value="1.fasta"/>
+      <param name="minrepeat" value="10"/>
+      <param name="maxrepeat" value="10"/>
+      <param name="threshold" value="20"/>
+      <param name="mismatch" value="no"/>
+       <param name="uniform" value="no"/>
+      <param name="out_format1" value="table"/>
+      <output name="ofile2" file="emboss_etandem_out.table"/>
+    </test>
+  </tests>
+  <code file="emboss_format_corrector.py" />
+  <help>
+.. class:: warningmark
+
+The input dataset needs to be sequences.
+
+-----
+
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/etandem.html
+  </help>
+</tool>
+
+
diff --git a/tools/emboss_5/emboss_fuzznuc.xml b/tools/emboss_5/emboss_fuzznuc.xml
new file mode 100644
index 00000000000..aaf72491e44
--- /dev/null
+++ b/tools/emboss_5/emboss_fuzznuc.xml
@@ -0,0 +1,66 @@
+<tool id="EMBOSS_fuzznuc37" name="fuzznuc">
+  <description>Nucleic acid pattern search</description>
+  <command>fuzznuc -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command>
+  <inputs>
+    <param format="fasta" name="input1" type="data">
+      <label>Sequences</label>
+    </param>
+    <param name="pattern" size="5" type="text" value="">
+      <label>Search pattern</label>
+    </param>
+    <param name="mismatch" size="5" type="text" value="0">
+      <label>Number of mismatches</label>
+    </param>
+    <param name="complement" type="select">
+      <label>Search complementary strand</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="fuzznuc">Fuzznuc Output File</option>
+      <option value="srs">SRS</option>
+      <option value="table">Table</option>
+      <option value="tagseq">TagSeq</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="fuzznuc" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="pattern" value="AA"/>
+      <param name="mismatch" value="0"/>
+      <param name="complement" value="no"/>
+      <param name="out_format1" value="excel"/>
+      <output name="out_file1" file="emboss_fuzznuc_out.tabular"/>
+    </test>
+  </tests>
+  <code file="emboss_format_corrector.py" />
+  <help>
+
+.. class:: warningmark
+
+The input dataset needs to be sequences.
+
+-----
+
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzznuc.html
+  </help>
+</tool>