Mercurial > repos > iuc > multiqc
comparison fastp_plugin.xml @ 24:0771dee34cff draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
| author | iuc |
|---|---|
| date | Mon, 02 Sep 2024 14:22:19 +0000 |
| parents | |
| children | 24002c7e6092 |
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| 23:d01bcfd04189 | 24:0771dee34cff |
|---|---|
| 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> |