comparison emboss_fuzznuc.xml @ 11:0e2484b6829b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68

10:9b98d3d903c6

<tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.1">
  <description>Nucleic acid pattern search</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <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" type="text" value="">
      <label>Search pattern</label>
      <sanitizer>
        <valid initial="string.printable">
         <remove value="&apos;"/>
        </valid>
        <mapping initial="none">
          <add source="&apos;" target=""/>
        </mapping>
      </sanitizer>
    </param>
    <param name="mismatch" 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="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="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

------

**Citation**

For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_

If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
  </help>
</tool>

11:0e2484b6829b

<tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.2">
  <description>Nucleic acid pattern search</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>fuzznuc -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</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="table">Table</option>
      <option value="tagseq">TagSeq</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="fuzznuc" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="pattern" value="AA"/>

      <param name="complement" value="no"/>
      <param name="out_format1" value="excel"/>
      <output name="out_file1" file="emboss_fuzznuc_out.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>