comparison arriba_get_filters.xml @ 5:005b200c8841 draft

"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"

4:77021ad5037d

            <option value="GRCm38">GRCm38</option>
            <option value="mm10">mm10</option>
        </param>
    </inputs>
    <outputs>
        <data name="blacklist" format="tabular" label="${tool.name} ${arriba_reference_name} blacklist.tsv"/>
        <data name="known_fusions" format="tabular" label="${tool.name} ${arriba_reference_name} known_fusions.tsv"/>
        <data name="protein_domains" format="gff3" label="${tool.name} ${arriba_reference_name} protein_domains.gff3"/>
        <data name="cytobands" format="tabular" label="${tool.name} ${arriba_reference_name} cytobands.tsv"/>
    </outputs>
    <tests>
        <test>

                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
** Arriba **

Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions.
It is based on chimeric alignments found by the STAR RNA-Seq aligner.

.. _Arriba: https://arriba.readthedocs.io/en/latest/

]]></help>
    <expand macro="citations" />
</tool>

5:005b200c8841

            <option value="GRCm38">GRCm38</option>
            <option value="mm10">mm10</option>
        </param>
    </inputs>
    <outputs>
        <data name="blacklist" format="tabular.gz" label="${tool.name} ${arriba_reference_name} blacklist.tsv.gz"/>
        <data name="known_fusions" format="tabular.gz" label="${tool.name} ${arriba_reference_name} known_fusions.tsv.gz"/>
        <data name="protein_domains" format="gff3" label="${tool.name} ${arriba_reference_name} protein_domains.gff3"/>
        <data name="cytobands" format="tabular" label="${tool.name} ${arriba_reference_name} cytobands.tsv"/>
    </outputs>
    <tests>
        <test>

                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**Arriba Get Filters**

Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions.
It is based on chimeric alignments found by the STAR RNA-Seq aligner.

The **Arriba Get Filters** tool adds the following Arriba distribution input_files_ to your galaxy history:

  - blacklist
  - known_fusions
  - protein_domains
  - cytobands


.. _Arriba: https://arriba.readthedocs.io/en/latest/
.. _input_files: https://arriba.readthedocs.io/en/latest/input-files/

]]></help>
    <expand macro="citations" />
</tool>