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comparison fastqc_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="@FASTQC_COMMAND@"><![CDATA[
3 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
4 @CREATE_REPEAT_DIR_1@
5 #if str($repeat2.type) == "data"
6 #for $k, $file in enumerate($repeat2.input)
7 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
8 #set file_path = os.path.join($file_dir, 'fastqc_data.txt')
9 mkdir '$file_dir' &&
10 ln -s '$file' '$file_path' &&
11 #end for
12 #elif str($repeat2.type) == "theoretical_gc"
13 #for $file in $repeat2.input
14 @ESCAPE_IDENTIFIER@
15 #set file_path = os.path.join($repeat_dir, str($identifier) + '_fastqc_theoretical_gc')
16 ln -s '$file' '$file_path' &&
17 #end for
18 #end if
19 #end for
20 ]]></token>
21
22 <xml name="fastqc_form">
23 <repeat name="output" title="FastQC output" min="1">
24 <param name="type" type="select" label="Type of FastQC output?">
25 <option value="data">Raw data</option>
26 <option value="theoretical_gc">Theorectical GC</option>
27 </param>
28 <param name="input" type="data" format="txt" multiple="true" label="FastQC output">
29 <validator type="expression" message="MultiQC does not accept the HTML report generated by FastQC, only the Raw Data">value is not None and value.extension != "html"</validator>
30 </param>
31 </repeat>
32 </xml>
33
34 <!-- add here your test files and tests, the more stringent the better -->
35 <xml name="fastqc_test">
36 <test expect_num_outputs="3">
37 <repeat name="results">
38 <conditional name="software_cond">
39 <param name="software" value="fastqc" />
40 <repeat name="output">
41 <param name="type" value="data"/>
42 <param name="input" value="fastqc_1.txt,fastqc_2.txt"/>
43 </repeat>
44 </conditional>
45 </repeat>
46 <param name="title" value="Title of the report"/>
47 <param name="comment" value="Commment for the report"/>
48 <param name="flat" value="true"/>
49 <param name="export" value="true"/>
50 <output name="html_report">
51 <assert_contents>
52 <has_text text="Title of the report" />
53 <has_text text="Commment for the report" />
54 <has_text text="fastqc_seq_heatmap_key_t" />
55 </assert_contents>
56 </output>
57 <output name="stats">
58 <assert_contents>
59 <has_text text="poulet5_1"/>
60 <has_text text="poulet5_2"/>
61 <has_text text="FastQC_mqc_generalstats_fastqc_median_sequence_length"/>
62 <has_n_lines n="3"/>
63 <has_n_columns n="7"/>
64 </assert_contents>
65 </output>
66 <output_collection name="plots" type="list" count="7"/>
67 </test>
68 </xml>
69
70
71 </macros>