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comparison template_plugin.xml @ 24:f7e2f1eb3a16 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
author iuc
date Mon, 02 Sep 2024 14:22:54 +0000
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23:abfd8a6544d7 24:f7e2f1eb3a16
1 <macros>
2 <!--
3 This is the TEMPLATE macro for MultiQC
4 1. please copy this template_plugin.xml to your own file e.g. trimmomatic_plugin.xml
5 2. Replace `TEMPLATE` with the name of the plugin, e.g. `fastqc`. The tokens and xml-names need to be called `trimmomatic_form` or `TRIMMOMATIC_COMMAND`
6 3. import your new *_plugin.xml macro into the main multiqc.xml file at the top of the file
7 4. add a new option to the main select element, e.g. `<option value="trimmomatic">Trimmomatic</option>`
8 5. add the *_COMMAND token to the <command> section.
9 6. add the *_test macro to the test section.
10 7. remove all unused comments from your new file
11 -->
12 <token name="@TEMPLATE_COMMAND@"><![CDATA[
13 <!--This pattern is used to check the file content in the @CHECK_LN_FILE@ token. The pattern should be included in the file. -->
14 #set $pattern = "Trimmomatic"
15 @LN_FILES@f
16 ]]></token>
17 <xml name="TEMPLATE_form">
18 <!-- Please add here your input forms specific to your plugin. Keep the name as `input` if you have a single input.
19 If you have multiple inputs have a look at other plugins, e.g. fastqc
20 -->
21 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Trimmomatic" help="It should contain 'TTrimmomatic'"/>
22 </xml>
23 <!-- add here your test files and tests, the more stringent the better -->
24 <xml name="TEMPLATE_test">
25 <test expect_num_outputs="3">
26 <repeat name="results">
27 <conditional name="software_cond">
28 <param name="software" value="trimmomatic"/>
29 <param name="input" value="trimmomatic.txt"/>
30 </conditional>
31 </repeat>
32 <param name="title" value="Title of the report"/>
33 <param name="comment" value="Commment for the report"/>
34 <param name="flat" value="true"/>
35 <param name="export" value="true"/>
36 <output name="html_report">
37 <assert_contents>
38 <has_text text="Title of the report"/>
39 <has_text text="Commment for the report"/>
40 <has_text text="cutadapt_trimmed_sequences_plot"/>
41 <has_text text="All-in-one FASTQ preprocessor"/>
42 <has_text text="trimmomatic_plot"/>
43 </assert_contents>
44 </output>
45 <output name="stats">
46 <assert_contents>
47 <has_text text="dataset_33"/>
48 <has_text text="R1_fq"/>
49 <has_text text="result_right"/>
50 <has_text text="25839_merged"/>
51 <has_text text="C2"/>
52 <has_n_lines n="11"/>
53 <has_n_columns n="22"/>
54 </assert_contents>
55 </output>
56 <output_collection name="plots" type="list" count="29"/>
57 </test>
58 </xml>
59 </macros>