diff --git a/tools/emboss_5/emboss_epestfind.xml b/tools/emboss_5/emboss_epestfind.xml
new file mode 100644
index 00000000000..7186c866270
--- /dev/null
+++ b/tools/emboss_5/emboss_epestfind.xml
@@ -0,0 +1,64 @@
+
+ Finds PEST motifs as potential proteolytic cleavage sites
+ emboss_single_outputfile_wrapper.pl epestfind -sequence $input1 -goutfile $ofile2 -outfile $ofile1 -window $window -order $order -potential $potential -poor $poor
+ -invalid $invalid -map $map -graph png -auto
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ You can view the original documentation here_.
+
+ .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/epestfind.html
+
+
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_est2genome.xml b/tools/emboss_5/emboss_est2genome.xml
new file mode 100644
index 00000000000..6a24dc1696f
--- /dev/null
+++ b/tools/emboss_5/emboss_est2genome.xml
@@ -0,0 +1,102 @@
+
+ Align EST and genomic DNA sequences
+ est2genome -estsequence $input1 -genomesequence $input2 -outfile $out_file1 -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty
+ $splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. 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/est2genome.html
+
+
diff --git a/tools/emboss_5/emboss_extractfeat.xml b/tools/emboss_5/emboss_extractfeat.xml
new file mode 100644
index 00000000000..dbbae6fe3b7
--- /dev/null
+++ b/tools/emboss_5/emboss_extractfeat.xml
@@ -0,0 +1,95 @@
+
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_extractseq.xml b/tools/emboss_5/emboss_extractseq.xml
new file mode 100644
index 00000000000..07d8c781597
--- /dev/null
+++ b/tools/emboss_5/emboss_extractseq.xml
@@ -0,0 +1,67 @@
+
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_format_corrector.py b/tools/emboss_5/emboss_format_corrector.py
new file mode 100644
index 00000000000..a9b83ad7fde
--- /dev/null
+++ b/tools/emboss_5/emboss_format_corrector.py
@@ -0,0 +1,50 @@
+#EMBOSS format corrector
+
+import operator
+#from galaxy import datatypes
+
+#Properly set file formats after job run
+def exec_after_process( app, inp_data, out_data, param_dict,tool, stdout, stderr):
+#Properly set file formats before job run
+#def exec_before_job(trans, inp_data, out_data, param_dict,tool):
+ #why isn't items an ordered list?
+ items = out_data.items()
+ #lets sort it ourselves....
+ items = sorted(items, key=operator.itemgetter(0))
+ #items is now sorted...
+
+ #normal filetype correction
+ data_count=1
+ for name, data in items:
+ outputType = param_dict.get( 'out_format'+str(data_count), None )
+ #print "data_count",data_count, "name", name, "outputType", outputType
+ if outputType !=None:
+ if outputType == 'ncbi':
+ outputType = "fasta"
+ elif outputType == 'excel':
+ outputType = "tabular"
+ elif outputType == 'text':
+ outputType = "txt"
+ data = app.datatypes_registry.change_datatype(data, outputType)
+ data.flush()
+ data_count+=1
+
+ #html filetype correction
+ data_count=1
+ for name, data in items:
+ wants_plot = param_dict.get( 'html_out'+str(data_count), None )
+ ext = "html"
+ if wants_plot == "yes":
+ data = app.datatypes_registry.change_datatype(data, ext)
+ data.flush()
+ data_count+=1
+
+ #png file correction
+ data_count=1
+ for name, data in items:
+ wants_plot = param_dict.get( 'plot'+str(data_count), None )
+ ext = "png"
+ if wants_plot == "yes":
+ data = app.datatypes_registry.change_datatype(data, ext)
+ data.flush()
+ data_count+=1
diff --git a/tools/emboss_5/emboss_freak.xml b/tools/emboss_5/emboss_freak.xml
new file mode 100644
index 00000000000..494997c603a
--- /dev/null
+++ b/tools/emboss_5/emboss_freak.xml
@@ -0,0 +1,35 @@
+
+ Residue/base frequency table or plot
+ freak -seqall $input1 -outfile $out_file1 -window $window -letters $letters -graph png -step $step -auto
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ You can view the original documentation here_.
+
+ .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/freak.html
+
+
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_fuzzpro.xml b/tools/emboss_5/emboss_fuzzpro.xml
new file mode 100644
index 00000000000..1e6e55f5240
--- /dev/null
+++ b/tools/emboss_5/emboss_fuzzpro.xml
@@ -0,0 +1,43 @@
+
+ Protein pattern search
+ fuzzpro -sequence $input1 -outfile $out_file1 -pattern "$pattern" -mismatch $mismatch -rformat2 $out_format1 -auto
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+