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comparison samtools_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="@SAMTOOLS_COMMAND@"><![CDATA[
3 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
4 @CREATE_REPEAT_DIR_2@
5 #if str($repeat2.type.type) == "stats"
6 #set $pattern = "This file was produced by samtools stats"
7 @LN_3_FILES@
8 #elif str($repeat2.type.type) == "flagstat"
9 #set $pattern = "in total (QC-passed reads + QC-failed reads)"
10 @LN_3_FILES@
11 #elif str($repeat2.type.type) == "idxstats"
12 #for $file in $repeat2.type.input
13 @ESCAPE_IDENTIFIER@
14 #set file_path = os.path.join($repeat_dir, str($identifier) + '_idxstat')
15 ln -s '$file' '$file_path' &&
16 #end for
17 #elif str($repeat2.type.type) == "rmdup"
18 #set $pattern = "[bam_rmdup"
19 @LN_3_FILES@
20 #end if
21 #end for
22 ]]></token>
23 <xml name="samtools_form">
24 <repeat name="output" title="Samtools output" min="1">
25 <conditional name="type">
26 <param name="type" type="select" label="Type of Samtools output?">
27 <option value="stats">stats</option>
28 <option value="flagstat">flagstat</option>
29 <option value="idxstats">idxstats</option>
30 <option value="rmdup">rmdup</option>
31 </param>
32 <when value="stats">
33 <param name="input" type="data" format="txt" multiple="true" label="Samtools stats output" help="It should contain 'This file was produced by samtools stats'"/>
34 </when>
35 <when value="flagstat">
36 <param name="input" type="data" format="txt" multiple="true" label="Samtools flagstat output" help="It should contain 'in total (QC-passed reads + QC-failed reads)'"/>
37 </when>
38 <when value="idxstats">
39 <param name="input" type="data" format="txt" multiple="true" label="Samtools idxstats output"/>
40 </when>
41 <when value="rmdup">
42 <param name="input" type="data" format="txt" multiple="true" label="Samtools rmdup output" help="It should contain '[bam_rmdup'"/>
43 </when>
44 </conditional>
45 </repeat>
46 </xml>
47 <!-- add here your test files and tests, the more stringent the better -->
48 <xml name="samtools_test">
49 <test expect_num_outputs="3">
50 <repeat name="results">
51 <conditional name="software_cond">
52 <param name="software" value="samtools"/>
53 <repeat name="output">
54 <conditional name="type">
55 <param name="type" value="stats"/>
56 <param name="input" value="samtools_stats.txt"/>
57 </conditional>
58 </repeat>
59 <repeat name="output">
60 <conditional name="type">
61 <param name="type" value="flagstat"/>
62 <param name="input" value="samtools_flagstat.txt"/>
63 </conditional>
64 </repeat>
65 <repeat name="output">
66 <conditional name="type">
67 <param name="type" value="idxstats"/>
68 <param name="input" value="samtools_idxstats.txt"/>
69 </conditional>
70 </repeat>
71 </conditional>
72 </repeat>
73 <param name="title" value="Title of the report"/>
74 <param name="comment" value="Commment for the report"/>
75 <param name="flat" value="true"/>
76 <param name="export" value="true"/>
77 <output name="html_report">
78 <assert_contents>
79 <has_text text="Title of the report"/>
80 <has_text text="Commment for the report"/>
81 <has_text text="samtools-flagstat-dp"/>
82 </assert_contents>
83 </output>
84 <output name="stats">
85 <assert_contents>
86 <has_text text="samtools_flagstat_txt"/>
87 <has_text text="mapped_passed"/>
88 <has_text text="stats_mqc_generalstats_samtools_stats_error_rate"/>
89 <has_text text="samtools_stats_txt"/>
90 <has_n_lines n="3"/>
91 <has_n_columns n="11"/>
92 </assert_contents>
93 </output>
94 <output_collection name="plots" type="list" count="5"/>
95 </test>
96 </xml>
97 </macros>