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comparison salmon_plugin.xml @ 24:0771dee34cff draft

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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 14:22:19 +0000
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23:d01bcfd04189 24:0771dee34cff
1 <macros>
2 <!-- not yet finished -->
3 <token name="@SALMON_COMMAND@"><![CDATA[
4 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
5 @CREATE_REPEAT_DIR_2@
6 #if str($repeat2.type.type) == "meta"
7 #for $k, $file in enumerate($repeat2.type.input)
8 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
9 #set file_path = os.path.join($file_dir, 'meta_info.json')
10 mkdir '$file_dir' &&
11 ln -s '$file' '$file_path' &&
12 #end for
13 #elif str($repeat2.type.type) == "fld"
14 #for $k, $file in enumerate($repeat2.type.input)
15 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
16 #set file_path = os.path.join($file_dir,'flenDist.txt')
17 mkdir '$file_dir' &&
18 ln -s '$file' '$file_path' &&
19 #end for
20 #end if
21 #end for
22 ]]></token>
23 <xml name="salmon_form">
24
25 </xml>
26 <!-- add here your test files and tests, the more stringent the better -->
27 <xml name="salmon_test">
28 <test expect_num_outputs="3">
29 <repeat name="results">
30 <conditional name="software_cond">
31 <param name="software" value="trimmomatic"/>
32 <param name="input" value="trimmomatic.txt"/>
33 </conditional>
34 </repeat>
35 <param name="title" value="Title of the report"/>
36 <param name="comment" value="Commment for the report"/>
37 <param name="flat" value="true"/>
38 <param name="export" value="true"/>
39 <output name="html_report">
40 <assert_contents>
41 <has_text text="Title of the report"/>
42 <has_text text="Commment for the report"/>
43 <has_text text="cutadapt_trimmed_sequences_plot"/>
44 <has_text text="All-in-one FASTQ preprocessor"/>
45 <has_text text="trimmomatic_plot"/>
46 </assert_contents>
47 </output>
48 <output name="stats">
49 <assert_contents>
50 <has_text text="dataset_33"/>
51 <has_text text="R1_fq"/>
52 <has_text text="result_right"/>
53 <has_text text="25839_merged"/>
54 <has_text text="C2"/>
55 <has_n_lines n="11"/>
56 <has_n_columns n="22"/>
57 </assert_contents>
58 </output>
59 <output_collection name="plots" type="list" count="29"/>
60 </test>
61 </xml>
62 </macros>