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comparison macros.xml @ 5:f9d3b5a6ef31 draft

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"planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2"
author iuc
date Thu, 12 Sep 2019 12:42:17 -0400
parents 4eb9595bff60
children 493a80c7107e
comparison
equal deleted inserted replaced
4:98413117ca70 5:f9d3b5a6ef31
8 8
9 <xml name="version_command"> 9 <xml name="version_command">
10 <version_command><![CDATA[snippy --version]]></version_command> 10 <version_command><![CDATA[snippy --version]]></version_command>
11 </xml> 11 </xml>
12 12
13 <token name="@VERSION@">4.3.6</token> 13 <token name="@REFERENCE_SOURCE_FILE@">
14 <![CDATA[
15 #if $reference_source.reference_source_selector == 'history'
16 #if $reference_source.ref_file.is_of_type("fasta")
17 ln -sf '$reference_source.ref_file' 'ref.fna' &&
18 #elif $reference_source.ref_file.is_of_type("genbank")
19 ln -sf '$reference_source.ref_file' 'ref.gbk' &&
20 #end if
21 #elif $reference_source.reference_source_selector == 'cached'
22 ln -sf '$reference_source.ref_file.fields.path' 'ref.fna' &&
23 #end if]]>
24 </token>
25
26 <token name="@REFERENCE_COMMAND@">
27 <![CDATA[
28 #if $reference_source.reference_source_selector == 'history'
29 #if $reference_source.ref_file.is_of_type("fasta")
30 --ref 'ref.fna'
31 #elif $reference_source.ref_file.is_of_type("genbank")
32 --ref 'ref.gbk'
33 #end if
34 #elif $reference_source.reference_source_selector == 'cached'
35 --ref 'ref.fna'
36 #end if
37 ]]>
38 </token>
39
40 <xml name="reference_selector">
41 <conditional name="reference_source">
42 <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.">
43 <option value="cached">Use a built-in genome index</option>
44 <option value="history">Use a genome from history and build index</option>
45 </param>
46 <when value="cached">
47 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
48 <options from_data_table="all_fasta">
49 <validator type="no_options" message="No reference genomes are available" />
50 </options>
51 </param>
52 </when>
53 <when value="history">
54 <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" />
55 </when>
56 </conditional>
57 </xml>
58
59 <token name="@VERSION@">4.4.3</token>
14 60
15 <xml name="citations"> 61 <xml name="citations">
16 <citations> 62 <citations>
17 <citation type="bibtex">@UNPUBLISHED{Seemann2013, 63 <citation type="bibtex">@UNPUBLISHED{Seemann2013,
18 author = "Seemann T", 64 author = "Seemann T",