comparison macros_last.xml @ 7:eca7ac1eb423 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit ddb5e058a7877e627ed24ef8cb9a046ccb450cb4

6:19c265784f35

<macros>
    <token name="@TOOL_VERSION@">1205</token>
    <token name="@LAST_HELP@"><![CDATA[
        Documentation : http://last.cbrc.jp/

        LAST finds similar regions between sequences.

        The main technical innovation is that LAST finds initial matches based on their multiplicity, instead of using a fixed length (e.g. BLAST uses 11-mers). To find these variable-length matches, it uses a suffix array (inspired by Vmatch). To achieve high sensitivity, it uses a spaced suffix array (or subset suffix array), analogous to spaced seeds (or subset seeds).

            - Calculate the likelihood of chance similarities between random sequences.
            - Do split and spliced alignment.
            - Train alignment parameters for unusual kinds of sequence (e.g. nanopore).

    ]]></token>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">last</xref>
        </xrefs>
    </xml>

            <param name="db_opts_input" type="select" label="Reference database">
              <option value="db">Locally installed LAST database</option>
              <option value="lastdb" selected="true">LAST database from history</option>
            </param>
            <when value="db">
                <param name="database" type="select" multiple="true" label="LAST database">
                    <options from_data_table="lastdb" />
                </param>
            </when>
            <when value="lastdb">
                <param name="lastdatabase" type="data" format="lastdb" label="LAST database" />

7:eca7ac1eb423

<macros>
    <token name="@TOOL_VERSION@">1205</token>
    <token name="@LAST_HELP@"><![CDATA[
        Documentation : https://gitlab.com/mcfrith/last

        LAST finds similar regions between sequences.

        The main technical innovation is that LAST finds initial matches based on their multiplicity, instead of using a fixed length (e.g. BLAST uses 11-mers). To find these variable-length matches, it uses a suffix array (inspired by Vmatch). To achieve high sensitivity, it uses a spaced suffix array (or subset suffix array), analogous to spaced seeds (or subset seeds).

            - Calculate the likelihood of chance similarities between random sequences.
            - Do split and spliced alignment.
            - Train alignment parameters for unusual kinds of sequence (e.g. nanopore).

    ]]></token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">last</requirement>
        </requirements>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">last</xref>
        </xrefs>
    </xml>

            <param name="db_opts_input" type="select" label="Reference database">
              <option value="db">Locally installed LAST database</option>
              <option value="lastdb" selected="true">LAST database from history</option>
            </param>
            <when value="db">
                <param name="database" type="select" label="LAST database">
                    <options from_data_table="lastdb" />
                </param>
            </when>
            <when value="lastdb">
                <param name="lastdatabase" type="data" format="lastdb" label="LAST database" />