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comparison rseqc_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="@RSEQC_COMMAND@"><![CDATA[
3 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
4 @CREATE_REPEAT_DIR_2@
5 #if str($repeat2.type.type) == "bam_stat"
6 #set $pattern = "Proper-paired reads map to different chrom:"
7 @LN_3_FILES@
8 #elif str($repeat2.type.type) == "gene_body_coverage"
9 #for $k, $file in enumerate($repeat2.type.input)
10 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.geneBodyCoverage.txt')
11 ln -s '$file' '$file_path' &&
12 #end for
13 #elif str($repeat2.type.type) == "inner_distance"
14 #for $k, $file in enumerate($repeat2.type.input)
15 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.inner_distance_freq.txt')
16 ln -s '${file}' '$file_path' &&
17 #end for
18 #elif str($repeat2.type.type) == "junction_annotation"
19 #set $pattern = "Partial Novel Splicing Junctions:"
20 @LN_3_FILES@
21 #elif str($repeat2.type.type) == "read_gc"
22 #for $k, $file in enumerate($repeat2.type.input)
23 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.GC.xls')
24 ln -s '$file' '$file_path' &&
25 #end for
26 #elif str($repeat2.type.type) == "junction_saturation"
27 #for $k, $file in enumerate($repeat2.type.input)
28 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.junctionSaturation_plot.r')
29 ln -s '${file}' '$file_path' &&
30 #end for
31 #elif str($repeat2.type.type) == "read_distribution"
32 #set $pattern = "Group Total_bases Tag_count Tags/Kb"
33 @LN_3_FILES@
34 #elif str($repeat2.type.type) == "read_duplication_pos"
35 #for $k, $file in enumerate($repeat2.type.input)
36 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.pos.DupRate.xls')
37 ln -s '$file' '$file_path' &&
38 #end for
39 #elif str($repeat2.type.type) == "infer_experiment"
40 #set $pattern = "Fraction of reads explained by"
41 #for $file in $repeat2.type.input
42 @ESCAPE_IDENTIFIER@
43 #set file_path = os.path.join($repeat_dir, str($identifier))
44 grep -q "$pattern" $file || die "'$pattern' not found in the file" &&
45 ln -s '$file' '$file_path' &&
46 #end for
47 #end if
48 #end for
49 ]]></token>
50 <xml name="rseqc_form">
51 <repeat name="output" title="RSeQC output" min="1">
52 <conditional name="type">
53 <param name="type" type="select" label="Type of RSeQC output?">
54 <option value="bam_stat">BAM/SAM mapping stats</option>
55 <option value="gene_body_coverage">Gene body coverage</option>
56 <option value="infer_experiment">Infer experiment</option>
57 <option value="inner_distance">Inner distance</option>
58 <option value="junction_annotation">Junction annotation</option>
59 <option value="junction_saturation">Junction saturation</option>
60 <option value="read_distribution">Read distribution</option>
61 <option value="read_duplication_pos">Read duplication</option>
62 <option value="read_gc">Read GC</option>
63 </param>
64 <when value="bam_stat">
65 <param name="input" type="data" format="txt,tabular" label="RSeQC BAM stat: output file" help="It should contain 'Proper-paired reads map to different chrom:" multiple="true"/>
66 </when>
67 <when value="gene_body_coverage">
68 <param name="input" type="data" format="txt" label="RSeQC gene body coverage: stats file" multiple="true"/>
69 </when>
70 <when value="infer_experiment">
71 <param name="input" type="data" format="txt" label="RSeQC infer experiment: configuration output" help="It should contain 'Fraction of reads explained by" multiple="true"/>
72 </when>
73 <when value="inner_distance">
74 <param name="input" type="data" format="txt" label="RSeQC inner distance: frequency file" multiple="true"/>
75 </when>
76 <when value="junction_annotation">
77 <param name="input" type="data" format="txt" label="RSeQC junction annotation: stats file" help="It should contain 'Partial Novel Splicing Junctions:" multiple="true"/>
78 </when>
79 <when value="junction_saturation">
80 <param name="input" type="data" format="txt" label="RSeQC junction saturation: junction saturation plot Rscript file" multiple="true"/>
81 </when>
82 <when value="read_distribution">
83 <param name="input" type="data" format="txt" label="RSeQC read distribution: stats output" help="It should contain 'Group Total_bases Tag_count Tags/Kb" multiple="true"/>
84 </when>
85 <when value="read_duplication_pos">
86 <param name="input" type="data" format="xls" label="RSeQC read duplication: positions XLS file" multiple="true"/>
87 </when>
88 <when value="read_gc">
89 <param name="input" type="data" format="csv,xls,tabular" label="RSeQC read GC output" multiple="true"/>
90 </when>
91 </conditional>
92 </repeat>
93 </xml>
94 <xml name="rseqc_test">
95 <test expect_num_outputs="3">
96 <repeat name="results">
97 <conditional name="software_cond">
98 <param name="software" value="rseqc"/>
99 <repeat name="output">
100 <conditional name="type">
101 <param name="type" value="junction_annotation"/>
102 <param name="input" value="junction_annotation.txt"/>
103 </conditional>
104 </repeat>
105 <repeat name="output">
106 <conditional name="type">
107 <param name="type" value="junction_saturation"/>
108 <param name="input" value="junction_saturation.txt"/>
109 </conditional>
110 </repeat>
111 </conditional>
112 </repeat>
113 <param name="title" value="Title of the report"/>
114 <param name="comment" value="Commment for the report"/>
115 <param name="flat" value="true"/>
116 <param name="export" value="true"/>
117 <output name="html_report">
118 <assert_contents>
119 <has_text text="Title of the report"/>
120 <has_text text="Commment for the report"/>
121 <has_text text="rseqc_junction_annotation"/>
122 <has_text text="rseqc_junction_annotation_junctions_plot"/>
123 </assert_contents>
124 </output>
125 <!-- for unknown reason empty
126 <output name="stats">
127 <assert_contents>
128 </assert_contents>
129 </output> -->
130 <output_collection name="plots" type="list" count="5"/>
131 </test>
132 </xml>
133 </macros>