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comparison dr-disco_classify.xml @ 3:5348cfd3ba5c draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
author erasmus-medical-center
date Thu, 10 Aug 2017 05:38:27 -0400
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children 922b52cf9b35
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2:173ca9768e22 3:5348cfd3ba5c
1 <tool id="dr_disco_classify" name="Dr. Disco (classify)" version="@TOOL_VERSION@-g0">
2 <description>Classifies detected break-points in RNA-seq based on corresponding statistics and blacklists</description>
3
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7
8 <expand macro="requirements"/>
9 <expand macro="version_command"/>
10
11 <command detect_errors="exit_code"><![CDATA[
12 dr-disco
13 classify
14
15 ${only_valid}
16
17 #if $blacklist_regions:
18 --blacklist-regions '${blacklist_regions}'
19 #end if
20
21 #if $blacklist_junctions:
22 --blacklist-junctions '${blacklist_junctions}'
23 #end if
24
25 '${dr_disco_detect_output}'
26 '${dr_disco_classify_output}'
27 ]]></command>
28
29 <inputs>
30 <param name="dr_disco_detect_output" type="data" format="tabular" label="Output of Dr. Disco Detect" />
31 <param name="only_valid" argument="--only-valid" truevalue="--only-valid" falsevalue="" type="boolean" />
32
33 <param name="blacklist_regions" argument="--blacklist-regions" type="data" format="bed" optional="True" label="Blacklist Regions" help="List of regions known to be false positives (https://github.com/yhoogstrate/dr-disco/tree/master/share/)" />
34 <param name="blacklist_junctions" argument="--blacklist-junctions" type="data" format="tabular" optional="True" label="Blacklist Junctions" help="List of junctions know to be false positives (https://github.com/yhoogstrate/dr-disco/tree/master/share/)" />
35 </inputs>
36
37 <outputs>
38 <data name="dr_disco_classify_output" format="tabular" label="${tool.name} on ${dr_disco_detect_output.name}" />
39 </outputs>
40
41 <tests>
42 <test>
43 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
44 <param name="only_valid" value="" />
45
46 <output name="dr_disco_classify_output" file="classify_test_16.test-01.out.dbed" ftype="tabular" />
47 </test>
48 <test>
49 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
50 <param name="only_valid" value="--only-valid" />
51
52 <output name="dr_disco_classify_output" file="classify_test_16.test-02.out.dbed" />
53 </test>
54
55 <test>
56 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
57 <param name="only_valid" />
58 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />
59
60 <output name="dr_disco_classify_output" file="classify_test_16.test-03.out.dbed" ftype="tabular" />
61 </test>
62 <test>
63 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
64 <param name="only_valid" />
65 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />
66
67 <output name="dr_disco_classify_output" file="classify_test_16.test-04.out.dbed" />
68 </test>
69
70 <test>
71 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
72 <param name="only_valid" />
73 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" />
74
75 <output name="dr_disco_classify_output" file="classify_test_16.test-05.out.dbed" ftype="tabular" />
76 </test>
77 <test>
78 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
79 <param name="only_valid" />
80 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" />
81
82 <output name="dr_disco_classify_output" file="classify_test_16.test-06.out.dbed" />
83 </test>
84
85 <test>
86 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
87 <param name="only_valid" />
88 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />
89 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" />
90
91 <output name="dr_disco_classify_output" file="classify_test_16.test-07.out.dbed" ftype="tabular" />
92 </test>
93 <test>
94 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
95 <param name="only_valid" />
96 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />
97 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" />
98
99 <output name="dr_disco_classify_output" file="classify_test_16.test-08.out.dbed" />
100 </test>
101 </tests>
102
103 <help><![CDATA[
104
105 **What it does**
106
107
108
109 **Attributions**
110
111 This work is part of Youri Hoogstrate's PhD thesis.
112
113 ]]></help>
114
115 <expand macro="citations"/>
116 </tool>