comparison cutadapt_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
date Mon, 02 Sep 2024 14:22:54 +0000
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23:abfd8a6544d7 24:f7e2f1eb3a16
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>