Mercurial > repos > iuc > multiqc
comparison template_plugin.xml @ 24:f7e2f1eb3a16 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
author | iuc |
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date | Mon, 02 Sep 2024 14:22:54 +0000 |
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23:abfd8a6544d7 | 24:f7e2f1eb3a16 |
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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> |