<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>