Mercurial > repos > iuc > multiqc
comparison cutadapt_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="@CUTADAPT_COMMAND@"><![CDATA[ | |
| 3 #set $pattern = "This is cutadapt" | |
| 4 #for $file in $repeat.software_cond.input | |
| 5 @ESCAPE_IDENTIFIER@ | |
| 6 #set file_path = os.path.join($software_dir, str($identifier) + '.txt') | |
| 7 ln -s '$file' '$file_path' && | |
| 8 ## replace header for old cutadapt release | |
| 9 sed -i.old 's/You are running/This is/' '$file_path' && | |
| 10 grep -q "$pattern" '$file_path' || die "'$pattern' or 'You are running cutadapt' not found in the file" && | |
| 11 #end for | |
| 12 ]]></token> | |
| 13 <xml name="cutadapt_form"> | |
| 14 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Cutadapt" help="It should contain 'This is cutadapt' or 'You are running cutadapt'"/> | |
| 15 </xml> | |
| 16 <xml name="cutadapt_test"> | |
| 17 <test expect_num_outputs="3"> | |
| 18 <repeat name="results"> | |
| 19 <conditional name="software_cond"> | |
| 20 <param name="software" value="cutadapt"/> | |
| 21 <param name="input" value="cutadapt.txt"/> | |
| 22 </conditional> | |
| 23 </repeat> | |
| 24 <param name="title" value="Title of the report"/> | |
| 25 <param name="comment" value="Commment for the report"/> | |
| 26 <param name="flat" value="true"/> | |
| 27 <param name="export" value="true"/> | |
| 28 <output name="html_report"> | |
| 29 <assert_contents> | |
| 30 <has_text text="Title of the report"/> | |
| 31 <has_text text="Commment for the report"/> | |
| 32 <has_text text="cutadapt_trimmed_sequences_plot"/> | |
| 33 </assert_contents> | |
| 34 </output> | |
| 35 <output name="stats"> | |
| 36 <assert_contents> | |
| 37 <has_text text="Cutadapt"/> | |
| 38 <has_text text="Cutadapt_mqc_generalstats_cutadapt_percent_trimmed"/> | |
| 39 <has_text text="10"/> | |
| 40 <has_text text="Cutadapt_mqc_generalstats_cutadapt_percent_trimmed"/> | |
| 41 <has_n_lines n="2"/> | |
| 42 <has_n_columns n="2"/> | |
| 43 </assert_contents> | |
| 44 </output> | |
| 45 <output_collection name="plots" type="list" count="2"/> | |
| 46 </test> | |
| 47 </xml> | |
| 48 </macros> |