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macros.xml
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macros.xml
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<macros>
<token name="@MIMODD_VERSION_REQUIRED@">0.1.9</token>
<token name="@MIMODD_REAL_VERSION@">0.1.9</token>
<token name="@MIMODD_WRAPPER_VERSION@">0.1.9</token>
<token name="@HELP_FOOTER@"><![CDATA[
----
.. class:: infomark
For **additional help** see these resources:
- The complete `MiModD User Guide <http://mimodd.readthedocs.io/en/doc0.1.9/usage_toc.html>`__
- The `MiModD help forum <https://groups.google.com/forum/#!forum/mimodd>`__ reachable also via `email <mailto:[email protected]>`__
]]></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) < 127 for c in value)</validator>
<sanitizer invalid_char="">
<valid initial="string.printable">
<remove preset="string.whitespace" value="'" />
<add value=" " />
</valid>
<mapping initial="none">
<add source="'" target="'"'"'" />
<add source="	" target=" " />
<add source=" " target=" " />
<add source=" " target=" " />
</mapping>
</sanitizer>
</macro>
</macros>