view emboss_cpgreport.xml @ 14:27c43fb015f0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753

<tool id="EMBOSS: cpgreport16" name="cpgreport" version="@VERSION@.1">
  <description>Reports all CpG rich regions</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command><![CDATA[
    cpgreport
      -sequence '$input1'
      -outfile '$out_file1'
      -outfeat '$out_file2'
      -offormat3 $out_format2
      -score $score
      -auto
  ]]>
  </command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="On query" />
    <param name="score" type="integer" min="1" max="200" value="17" label="Score for each CG sequence found" />
    <param name="out_format2" type="select" label="Output feature file format">
      <option value="gff">GFF</option>
      <option value="embl">EMBL</option>
      <option value="swiss">SwissProt</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="cpgreport" />
    <data name="out_file2" format="gff" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="score" value="17"/>
      <param name="out_format2" value="embl"/>
      <output name="out_file1" file="emboss_cpgreport_out2.cpgreport"/>
    </test>
    <!-- <test>
      <param name="input1" value="2.fasta"/>
      <param name="score" value="17"/>
      <param name="out_format2" value="gff"/>
      <output name="out_file1" file="emboss_cpgreport_out1.gff"/>
    </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/cpgreport.html
  </help>
  <expand macro="citations" />
</tool>