annotate macros.xml @ 2:9c5c2d4cf379 draft

planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312

<macros>
    <token name="@MIMODD_VERSION_REQUIRED@">0.1.8</token>
    <token name="@MIMODD_REAL_VERSION@">0.1.8</token>
    <token name="@MIMODD_WRAPPER_VERSION@">0.1.8_1</token>
    <token name="@HELP_FOOTER@"><![CDATA[
----

.. class:: infomark

   For **additional help** see these resources: 

- The complete `MiModD User Guide <http://mimodd.readthedocs.io/en/doc0.1.8/usage_toc.html>`__

- The `MiModD help forum <https://groups.google.com/forum/#!forum/mimodd>`__ reachable also via `email <mailto:[e-mail]>`__

   ]]></token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@MIMODD_VERSION_REQUIRED@">MiModD</requirement>
            <yield />
        </requirements>
    </xml>
    <xml name="stdio">
        <stdio>
            <exit_code range="1:" />
        </stdio>
    </xml>
    <xml name="version_command">
        <version_command><![CDATA[mimodd version -q]]></version_command>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
@misc{
maier_mimodd_2014,
title = {{MiModD} - {Mutation} {Identification} in {Model} {Organism} {Genomes}},
shorttitle = {{MiModD}},
url = {https://sourceforge.net/projects/mimodd/},
author = {Maier, Wolfgang and Moos, Katharina and Seifert, Mark and Baumeister, Ralf},
year = {2014}, publisher={SourceForge.net} }
            </citation>
        </citations>
    </xml>
    <macro name="YYYY-MM-DD_format_validator">
        <validator type="expression" message="YYYY-MM-DD date format required">not value or (len(value.split('-')) == 3 and all(part.isdigit() and len(part)==expect_len for part, expect_len in zip(value.split('-'), [4,2,2])))</validator>
    </macro>
    <macro name="known_sequencing_platform options">
        <option value="ILLUMINA">ILLUMINA</option>
        <option value="PACBIO">PACBIO</option>
        <option value="IONTORRENT">IONTORRENT</option>
        <option value="ONT">ONT</option>
        <option value="LS454">LS454</option>
        <option value="SOLID">SOLID</option>
        <option value="HELICOS">HELICOS</option>
        <option value="CAPILLARY">CAPILLARY</option>
    </macro>
    <macro name="lex_sam_header" token_message="SAM header data may not contain non-ASCII characters.">
        <validator type="expression" message="@MESSAGE@">not value or all(ord(c) &lt; 127 for c in value)</validator>
        <sanitizer invalid_char="">
            <valid initial="string.printable">
                <remove preset="string.whitespace" value="&#39;" />
                <add value=" " />
            </valid>
            <mapping initial="none">
                <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" />
                <add source="&#09;" target="&#32;" />
                <add source="&#10;" target="&#32;" />
                <add source="&#13;" target="&#32;" />
            </mapping>
        </sanitizer>
    </macro>
</macros>