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comparison star_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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children 24002c7e6092
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23:d01bcfd04189 24:0771dee34cff
1 <macros>
2 <token name="@STAR_COMMAND@"><![CDATA[
3 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
4 @CREATE_REPEAT_DIR_2@
5 #if str($repeat2.type.type) == "log"
6 #for $file in $repeat2.type.input
7 @ESCAPE_IDENTIFIER@
8 #set file_path = os.path.join($repeat_dir, str($identifier) + '_Log.final.out')
9 ln -s '$file' '$file_path' &&
10 #end for
11 #elif str($repeat2.type.type) == "genecounts"
12 #for $file in $repeat2.type.input
13 @ESCAPE_IDENTIFIER@
14 #set file_path = os.path.join($repeat_dir, str($identifier) + '_ReadsPerGene.out.tab')
15 ln -s '$file' '$file_path' &&
16 #end for
17 #end if
18 #end for
19 ]]></token>
20 <xml name="star_form">
21 <repeat name="output" title="STAR output" min="1">
22 <conditional name="type">
23 <param name="type" type="select" label="Type of STAR output?">
24 <option value="log">Log</option>
25 <option value="genecounts">Gene counts</option>
26 </param>
27 <when value="log">
28 <param name="input" type="data" format="txt" label="STAR log output" multiple="true"/>
29 </when>
30 <when value="genecounts">
31 <param name="input" type="data" format="tabular,tsv" label="STAR gene count output" multiple="true"/>
32 </when>
33 </conditional>
34 </repeat>
35 </xml>
36 <xml name="star_test">
37 <test expect_num_outputs="3">
38 <repeat name="results">
39 <conditional name="software_cond">
40 <param name="software" value="star"/>
41 <repeat name="output">
42 <conditional name="type">
43 <param name="type" value="log"/>
44 <param name="input" value="star_log.txt"/>
45 </conditional>
46 </repeat>
47 <repeat name="output">
48 <conditional name="type">
49 <param name="type" value="genecounts"/>
50 <param name="input" value="star_counts.txt"/>
51 </conditional>
52 </repeat>
53 </conditional>
54 </repeat>
55 <param name="title" value="Title of the report"/>
56 <param name="comment" value="Commment for the report"/>
57 <param name="flat" value="true"/>
58 <param name="export" value="true"/>
59 <output name="html_report">
60 <assert_contents>
61 <has_text text="Title of the report"/>
62 <has_text text="Commment for the report"/>
63 <has_text text="star_alignment_plot"/>
64 </assert_contents>
65 </output>
66 <output name="stats">
67 <assert_contents>
68 <has_text text="STAR_mqc_generalstats_star_uniquely_mapped_percent"/>
69 <has_text text="star_log_txt"/>
70 <has_n_lines n="2"/>
71 <has_n_columns n="7"/>
72 </assert_contents>
73 </output>
74 <output_collection name="plots" type="list" count="1"/>
75 </test>
76 </xml>
77 </macros>