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comparison fastp_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 <token name="@FASTP_COMMAND@"><![CDATA[
3 #set $pattern = "report_title"
4 #for $file in $repeat.software_cond.input
5 @ESCAPE_IDENTIFIER@
6 #set file_path = os.path.join($software_dir, str($identifier) + 'fastp.json')
7 ln -s '$file' '$file_path' &&
8 grep -q "$pattern" '$file_path' || die "'$pattern' or 'report_title' not found in the file" &&
9 #end for
10 ]]></token>
11 <xml name="fastp_form">
12 <param name="input" type="data" format="json" label="Output of fastp" help="It should be the json report from fastp containing 'report_title" multiple="true"/>
13 </xml>
14 <!-- add here your test files and tests, the more stringent the better -->
15 <xml name="fastp_test">
16 <test expect_num_outputs="3">
17 <repeat name="results">
18 <conditional name="software_cond">
19 <param name="software" value="fastp"/>
20 <param name="input" value="fastp1.json.txt,fastp2.json.txt"/>
21 </conditional>
22 </repeat>
23 <param name="title" value="Title of the report"/>
24 <param name="comment" value="Commment for the report"/>
25 <param name="flat" value="true"/>
26 <param name="export" value="true"/>
27 <output name="html_report">
28 <assert_contents>
29 <has_text text="Title of the report"/>
30 <has_text text="Commment for the report"/>
31 <has_text text="All-in-one FASTQ preprocessor"/>
32 </assert_contents>
33 </output>
34 <output name="stats">
35 <assert_contents>
36 <has_text text="fastp_mqc_generalstats_fastp_pct_duplication"/>
37 <has_text text="R1_fq"/>
38 <has_text text="fastp_mqc_generalstats_fastp_after_filtering_q30_rate"/>
39 <has_text text="bwa-mem-fastq1_fq"/>
40 <has_n_lines n="3"/>
41 <has_n_columns n="8"/>
42 </assert_contents>
43 </output>
44 <output_collection name="plots" type="list" count="15"/>
45 </test>
46 </xml>
47 </macros>