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macros.xml
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macros.xml
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<macros>
<xml name="requirements">
<requirements>
<requirement type="package" version="@VERSION@">snippy</requirement>
<requirement type="package" version="1.32">tar</requirement>
<yield />
</requirements>
</xml>
<xml name="version_command">
<version_command><![CDATA[snippy --version]]></version_command>
</xml>
<token name="@REFERENCE_SOURCE_FILE@">
<![CDATA[
#if $reference_source.reference_source_selector == 'history'
#if $reference_source.ref_file.is_of_type("fasta")
ln -sf '$reference_source.ref_file' 'ref.fna' &&
#elif $reference_source.ref_file.is_of_type("genbank")
ln -sf '$reference_source.ref_file' 'ref.gbk' &&
#end if
#elif $reference_source.reference_source_selector == 'cached'
ln -sf '$reference_source.ref_file.fields.path' 'ref.fna' &&
#end if]]>
</token>
<token name="@REFERENCE_COMMAND@">
<![CDATA[
#if $reference_source.reference_source_selector == 'history'
#if $reference_source.ref_file.is_of_type("fasta")
--ref 'ref.fna'
#elif $reference_source.ref_file.is_of_type("genbank")
--ref 'ref.gbk'
#end if
#elif $reference_source.reference_source_selector == 'cached'
--ref 'ref.fna'
#end if
]]>
</token>
<xml name="reference_selector">
<conditional name="reference_source">
<param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below. If you would like to perform self-mapping select `history` here, then choose your input file as reference.">
<option value="cached">Use a built-in genome index</option>
<option value="history">Use a genome from history and build index</option>
</param>
<when value="cached">
<param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
<options from_data_table="all_fasta">
<validator type="no_options" message="No reference genomes are available" />
</options>
</param>
</when>
<when value="history">
<param name="ref_file" type="data" format="fasta,genbank" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference" />
</when>
</conditional>
</xml>
<token name="@VERSION@">4.4.5</token>
<xml name="citations">
<citations>
<citation type="bibtex">@UNPUBLISHED{Seemann2013,
author = "Seemann T",
title = "snippy: fast bacterial variant calling from NGS reads",
year = "2015",
note = "https://github.com/tseemann/snippy",
url = "https://github.com/tseemann/snippy"}</citation>
</citations>
</xml>
</macros>