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comparison cooc_pubmut.xml @ 0:faaae22ddea8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
author iuc
date Thu, 11 Aug 2022 13:47:15 +0000
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children 06e4aed6a606
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1 <tool id="cooc_pubmut" name="Cojac: pubmut" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
2 profile="@PROFILE@">
3 <description>
4 render a JSON or YAML file to a pretty table
5 </description>
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9 <expand macro="biotools"/>
10 <expand macro="requirements">
11 <requirement type="package" version="2.12">pandoc</requirement>
12 </expand>
13 <expand macro="version"/>
14 <command detect_errors="exit_code"><![CDATA[
15 @VOCDIR_COMMAND@
16 #for $input_file in $cooc_file
17 #set $cooc_ext = $input_file.ext
18 #end for
19 cooc-pubmut
20 -m '$vocdir'
21 -a '$amplicons'
22 #if $cooc_ext == 'json'
23 -j '$cooc_file'
24 #else if $cooc_ext == 'yaml'
25 -y '$cooc_file'
26 #end if
27 -o cooc-table.csv
28 -q
29 $escape
30 #if $add_html
31 && pandoc cooc-table.csv -o cooc-table.html
32 && mkdir -p '$html.files_path'
33 && cp cooc-table.html '$html.files_path'
34 #end if
35 ]]></command>
36 <inputs>
37 <expand macro="vocdir_input"/>
38 <param name="amplicons" type="data" format="yaml" label="List of query amplicons"
39 help="File generated by the Cojac mutbamscan tool"/>
40 <param name="cooc_file" type="data" format="json,yaml" multiple="true"
41 label="Results generated by mutbamscan"/>
42 <param argument="--escape" type="boolean" truevalue="--escape" falsevalue=""
43 checked="false" label="Use escape characters for newlines"/>
44 <param name="add_html" type="boolean" checked="false"
45 label="Convert CSV output table to HTML format"/>
46 </inputs>
47 <outputs>
48 <data name="table" format="csv"
49 label="${tool.name} on ${on_string}: Mutation cooccurrence (CSV table)"
50 from_work_dir="cooc-table.csv">
51 </data>
52 <data name="html" format="html"
53 label="${tool.name} on ${on_string}: Mutation cooccurrence (HTML)"
54 from_work_dir="cooc-table.html">
55 <filter>add_html</filter>
56 </data>
57 </outputs>
58 <tests>
59 <test expect_num_outputs="1">
60 <conditional name="vocdir_option">
61 <param name="choice" value="custom"/>
62 <param name="voc_file" value="omicron_ba1_mutations.yaml"/>
63 </conditional>
64 <param name="amplicons" value="amplicons111.yaml"/>
65 <param name="cooc_file" value="cooc-test111.json"/>
66 <output name="table" ftype="csv">
67 <assert_contents>
68 <has_text text="Amplicon 76"/>
69 <has_text text="Amplicon 81"/>
70 </assert_contents>
71 </output>
72 </test>
73 </tests>
74 <help><![CDATA[
75 @HELP_HEADER@
76
77 Information about **cooc-pubmut** method
78 ========================================
79
80 The method renders a JSON or YAML file to a table as in the publication.
81 You need to open the output CSV in a spreadsheet that understands linebreaks.
82
83 ]]></help>
84 <expand macro="citations"/>
85 </tool>