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comparison nonpareil_plugin.xml @ 27:7591bce96601 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
author iuc
date Tue, 18 Feb 2025 23:18:25 +0000
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26:d2aaac19f42f 27:7591bce96601
1 <macros>
2 <token name="@NONPAREIL_COMMAND@"><![CDATA[
3 #set $pattern = "LRstar"
4 #for $file in $repeat.software_cond.input
5 @ESCAPE_IDENTIFIER@
6 #set file_path = os.path.join($software_dir, str($identifier) + '.json')
7 ln -s '$file' '$file_path' &&
8 #end for
9 ]]></token>
10 <xml name="nonpareil_form">
11 <param name="input" type="data" format="json" multiple="true" label="JSON object output of Nonpareil" help="It should contain 'LRstar'"/>
12 </xml>
13 <xml name="nonpareil_test">
14 <test expect_num_outputs="3">
15 <repeat name="results">
16 <conditional name="software_cond">
17 <param name="software" value="nonpareil"/>
18 <param name="input" value="nonpareil.json"/>
19 </conditional>
20 </repeat>
21 <param name="title" value="Title of the report"/>
22 <param name="comment" value="Commment for the report"/>
23 <param name="flat" value="true"/>
24 <param name="export" value="true"/>
25 <output name="html_report">
26 <assert_contents>
27 <has_text text="Title of the report"/>
28 <has_text text="Commment for the report"/>
29 <has_text text="Estimates metagenomic coverage and sequence diversity"/>
30 <has_text text="Nonpareil"/>
31 <has_text text="Redundancy levels"/>
32 <has_text text="21.3"/>
33 <has_text text="24.3"/>
34 </assert_contents>
35 </output>
36 <output name="stats">
37 <assert_contents>
38 <has_text text="nonpareil-nonpareil_R"/>
39 <has_text text="nonpareil-nonpareil_LR"/>
40 <has_text text="nonpareil-nonpareil_kappa"/>
41 <has_text text="nonpareil-nonpareil_C"/>
42 <has_text text="nonpareil-nonpareil_diversity"/>
43 <has_text text="11.9521"/>
44 <has_text text="0.0005"/>
45 <has_n_lines n="2"/>
46 <has_n_columns n="6"/>
47 </assert_contents>
48 </output>
49 <output_collection name="plots" type="list" count="3"/>
50 </test>
51 </xml>
52 </macros>