annotate macros.xml @ 10:3fe8ef358d66 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit 25b2375521fec3162644696b67e54f654fab2e79"
author iuc
date Thu, 30 Jan 2020 18:18:38 -0500
parents 32f2211eeec3
children 5bbf9eada9c2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
1 <macros>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
2 <xml name="requirements">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
3 <requirements>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
4 <requirement type="package" version="@VERSION@">snippy</requirement>
8
32f2211eeec3 "planemo upload commit 5b41fad964a75dcdc794e90342144c3eccea16d7"
iuc
parents: 6
diff changeset
5 <requirement type="package" version="1.32">tar</requirement>
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
6 <yield />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
7 </requirements>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
8 </xml>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
9
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
10 <xml name="version_command">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
11 <version_command><![CDATA[snippy --version]]></version_command>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
12 </xml>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
13
5
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
14 <token name="@REFERENCE_SOURCE_FILE@">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
15 <![CDATA[
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
16 #if $reference_source.reference_source_selector == 'history'
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
17 #if $reference_source.ref_file.is_of_type("fasta")
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
18 ln -sf '$reference_source.ref_file' 'ref.fna' &&
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
19 #elif $reference_source.ref_file.is_of_type("genbank")
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
20 ln -sf '$reference_source.ref_file' 'ref.gbk' &&
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
21 #end if
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
22 #elif $reference_source.reference_source_selector == 'cached'
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
23 ln -sf '$reference_source.ref_file.fields.path' 'ref.fna' &&
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
24 #end if]]>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
25 </token>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
26
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
27 <token name="@REFERENCE_COMMAND@">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
28 <![CDATA[
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
29 #if $reference_source.reference_source_selector == 'history'
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
30 #if $reference_source.ref_file.is_of_type("fasta")
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
31 --ref 'ref.fna'
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
32 #elif $reference_source.ref_file.is_of_type("genbank")
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
33 --ref 'ref.gbk'
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
34 #end if
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
35 #elif $reference_source.reference_source_selector == 'cached'
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
36 --ref 'ref.fna'
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
37 #end if
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
38 ]]>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
39 </token>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
40
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
41 <xml name="reference_selector">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
42 <conditional name="reference_source">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
43 <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.">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
44 <option value="cached">Use a built-in genome index</option>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
45 <option value="history">Use a genome from history and build index</option>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
46 </param>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
47 <when value="cached">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
48 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
49 <options from_data_table="all_fasta">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
50 <validator type="no_options" message="No reference genomes are available" />
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
51 </options>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
52 </param>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
53 </when>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
54 <when value="history">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
55 <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" />
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
56 </when>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
57 </conditional>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
58 </xml>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 2
diff changeset
59
6
4df82423ba61 "planemo upload commit 1235e6893a7e0d9ea3a600204c515fec1810dd93"
iuc
parents: 5
diff changeset
60 <token name="@VERSION@">4.4.5</token>
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
61
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
62 <xml name="citations">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
63 <citations>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
64 <citation type="bibtex">@UNPUBLISHED{Seemann2013,
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
65 author = "Seemann T",
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
66 title = "snippy: fast bacterial variant calling from NGS reads",
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
67 year = "2015",
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
68 note = "https://github.com/tseemann/snippy",
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
69 url = "https://github.com/tseemann/snippy"}</citation>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
70 </citations>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
71 </xml>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
72 </macros>