comparison segalign.xml @ 23:e9bf680c292b draft default tip

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit a2f684fa36d99b0d8d03f2b802d08b56b8545bc6

22:860e1f6f3de4

                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
    SegAlign is a scalable, GPU-accelerated system for computing pairwise WGA. SegAlign is based on the standard seed-filter-extend heuristic, in which the filtering stage dominates the runtime (e.g. 98% for human-mouse WGA), and is accelerated using GPU(s).

    https://github.com/gsneha26
    ]]></help>
    <expand macro="citations"/>
</tool>

23:e9bf680c292b

                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
SegAlign is a scalable, GPU-accelerated system for computing pairwise WGA. SegAlign is based on the standard seed-filter-extend heuristic, in which the filtering stage dominates the runtime (e.g. 98% for human-mouse WGA), and is accelerated using GPU(s). SegAlign was designed as a faster replacement for lastz pairwise aligner.

**Using this tool**

.. class:: warningmark

This tool is the first part of a two-step process for generation of paiwrise alignments. The output of this tool is used as an input to **Batched LASTZ** tool. The *Batched LASTZ** can be found in the list of tool of this Galaxy instance.

**What it does**

SegAlign processes **Target** and **Query** sequences to identify highly similar regions where gapped extension will be performed to create actual alignments. The actual alignments are generated by **Batched LASTZ** that should be run on the output of this tool.

.. class:: infomark

Although this tool is only the first part of the alignment process all parameters related to generation of alignments are set **during this stage**.

**Scoring Options**

By default the HOXD70 substitution scores are used (from `Chiaromonte et al. 2002 <https://www.ncbi.nlm.nih.gov/pubmed/11928468>`_)::

    bad_score          = X:-1000  # used for sub['X'][*] and sub[*]['X']
    fill_score         = -100     # used when sub[*][*] is not defined
    gap_open_penalty   =  400
    gap_extend_penalty =   30

         A     C     G     T
    A   91  -114   -31  -123
    C -114   100  -125   -31
    G  -31  -125   100  -114
    T -123   -31  -114    91

Matrix can be supplied as an input to **Read the substitution scores** parameter in *Scoring* section. Substitution matrix can be inferred from your data using another LASTZ-based tool (LASTZ_D: Infer substitution scores).

**Output Options**

.. class:: infomark

The final format in which alignmnets will be generated by **Batched LASTZ** are set here.

The default output is a MAF alignment file. Other formats can be configured in *Output Options* section.  See LASTZ manual <https://lastz.github.io/lastz/#formats>`_ for description of possible formats.
    ]]></help>
    <expand macro="citations"/>
</tool>