--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/emboss_fuzznuc.xml	Tue Jan 25 03:26:28 2022 +0000
@@ -0,0 +1,133 @@
+<tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="6.6.0">
+  <description>Nucleic acid pattern search</description>
+  <expand macro="bio_tools" />
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <code file="emboss_format_corrector.py" />
+  <command><![CDATA[
+    fuzznuc
+
+    -sequence '$input1'
+    $seq_qualifiers.sreverse1 $seq_qualifiers.snucleotide1 $seq_qualifiers.sprotein1 $seq_qualifiers.slower1 $seq_qualifiers.supper1 $seq_qualifiers.scircular1
+    #if $seq_qualifiers.sbegin1
+      -sbegin1 '$seq_qualifiers.sbegin1'
+    #end if
+    #if $seq_qualifiers.send1
+      -send1 '$seq_qualifiers.send1'
+    #end if
+    #if $seq_qualifiers.ioffset1
+      -ioffset1 '$seq_qualifiers.ioffset1'
+    #end if
+
+    -outfile '$out_file1'
+    $out_qualifiers.raccshow2 $out_qualifiers.rdesshow2 $out_qualifiers.rscoreshow2 $out_qualifiers.rusashow2 $out_qualifiers.rstrandshow2
+    #if $out_qualifiers.rmaxall2
+      -rmaxall2 '$out_qualifiers.rmaxall2'
+    #end if
+    #if $out_qualifiers.rmaxseq2
+      -rmaxseq2 '$out_qualifiers.rmaxseq2'
+    #end if
+
+    -pattern '$pattern' -pmismatch '$mismatch' -rformat2 '$out_format1' -auto
+
+    -complement '$complement'
+  ]]></command>
+  <inputs>
+    <param name="input1" type="data" format="fasta" label="Sequences" />
+    <param name="pattern" type="text" value="" label="Search pattern">
+      <sanitizer>
+        <valid initial="string.printable">
+         <remove value="&apos;"/>
+        </valid>
+        <mapping initial="none">
+          <add source="&apos;" target=""/>
+        </mapping>
+      </sanitizer>
+    </param>
+    <param name="mismatch" type="integer" value="0" label="Number of mismatches" />
+    <param name="complement" type="select" label="Search complementary strand">
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="out_format1" type="select" label="Output report file format">
+      <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>
+
+    <section name="seq_qualifiers" title="Sequence associated qualifiers">
+      <param type="integer" argument="-sbegin1" optional="true" label="Start of each sequence to be used"/>
+      <param type="integer" argument="-send1" optional="true" label="End of each sequence to be used"/>
+      <param type="integer" argument="-ioffset1" optional="true" label="Input start position offset"/>
+      <param type="boolean" argument="-sreverse1" truevalue="-sreverse1 Y" falsevalue="" label="Reverse (if DNA)"/>
+      <param type="boolean" argument="-snucleotide1" truevalue="-snucleotide1 Y" falsevalue="" label="Sequence is nucleotide"/>
+      <param type="boolean" argument="-sprotein1" truevalue="-sprotein1 Y" falsevalue="" label="Sequence is protein"/>
+      <param type="boolean" argument="-slower1" truevalue="-slower1 Y" falsevalue="" label="Make lower case"/>
+      <param type="boolean" argument="-supper1" truevalue="-supper1 Y" falsevalue="" label="Make upper case"/>
+      <param type="boolean" argument="-scircular1" truevalue="-scircular1 Y" falsevalue="" label="Sequence is circular"/>
+    </section>
+
+    <section name="out_qualifiers" title="Outfile associated qualifiers">
+      <param type="boolean" argument="-raccshow2" truevalue="-raccshow2 Y" falsevalue="" label="Show accession number in the report"/>
+      <param type="boolean" argument="-rdesshow2" truevalue="-rdesshow2 Y" falsevalue="" label="Show description in the report"/>
+      <param type="boolean" argument="-rscoreshow2" truevalue="-rscoreshow2 Y" falsevalue="" label="Show the score in the report"/>
+      <param type="boolean" argument="-rstrandshow2" truevalue="-rstrandshow2 Y" falsevalue="" label="Show the nucleotide strand in the report"/>
+      <param type="boolean" argument="-rusashow2" truevalue="-rusashow2 Y" falsevalue="" label="Show the full USA in the report"/>
+      <param type="integer" argument="-rmaxall2" optional="true" label="Maximum total hits to report"/>
+      <param type="integer" argument="-rmaxseq2" optional="true" label="Maximum hits to report for one sequence"/>
+    </section>
+
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="fuzznuc" />
+  </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>
+    <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"/>
+      <param name="seq_qualifiers|supper1" value="true"/>
+      <param name="seq_qualifiers|sbegin1" value="100"/>
+      <param name="out_qualifiers|rmaxseq2" value="5"/>
+      <output name="out_file1" file="emboss_fuzznuc_out2.tabular"/>
+    </test>
+  </tests>
+  <help>
+.. class:: warningmark
+
+The input dataset needs to be sequences.
+
+-----
+
+    You can view the original documentation here_.
+
+    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/fuzznuc.html
+  </help>
+  <expand macro="citations" />
+</tool>