Mercurial > repos > erasmus-medical-center > dr_disco

comparison dr-disco_classify.xml @ 10:f2c70d589596 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 3b03a60c8a46cc23f6fbbb9e32111b39c6044fad
author erasmus-medical-center
date Thu, 02 Nov 2017 05:17:31 -0400
parents 922b52cf9b35
children 3743fd602fa9
comparison
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9:c3ce472a315f 10:f2c70d589596
20 20
21 #if $blacklist_junctions: 21 #if $blacklist_junctions:
22 --blacklist-junctions '${blacklist_junctions}' 22 --blacklist-junctions '${blacklist_junctions}'
23 #end if 23 #end if
24 24
25 --min-chim-overhang '${min_chim_overhang}'
26
25 '${dr_disco_detect_output}' 27 '${dr_disco_detect_output}'
26 '${dr_disco_classify_output}' 28 '${dr_disco_classify_output}'
27 ]]></command> 29 ]]></command>
28 30
29 <inputs> 31 <inputs>
30 <param name="dr_disco_detect_output" type="data" format="tabular" label="Output of Dr. Disco Detect" /> 32 <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" /> 33 <param name="only_valid" argument="--only-valid" truevalue="--only-valid" falsevalue="" type="boolean" />
32 34
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/)" /> 35 <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/)" /> 36 <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/)" />
37
38 <param name="min_chim_overhang" type="integer" min="-1" value="50" label="Minimum alignment length on each side of the junction." help="May need to be set to smaller values for read lengths smaller than 75bp." argument="--min-chim-overhang" />
35 </inputs> 39 </inputs>
36 40
37 <outputs> 41 <outputs>
38 <data name="dr_disco_classify_output" format="tabular" label="${tool.name} on ${dr_disco_detect_output.name}" /> 42 <data name="dr_disco_classify_output" format="tabular" label="${tool.name} on ${dr_disco_detect_output.name}" />
39 </outputs> 43 </outputs>
43 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" /> 47 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
44 <param name="only_valid" value="" /> 48 <param name="only_valid" value="" />
45 49
46 <output name="dr_disco_classify_output" file="classify_test_16.test-01.out.dbed" ftype="tabular" /> 50 <output name="dr_disco_classify_output" file="classify_test_16.test-01.out.dbed" ftype="tabular" />
47 </test> 51 </test>
52
48 <test> 53 <test>
49 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" /> 54 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
50 <param name="only_valid" value="--only-valid" /> 55 <param name="only_valid" value="--only-valid" />
51 56
52 <output name="dr_disco_classify_output" file="classify_test_16.test-02.out.dbed" /> 57 <output name="dr_disco_classify_output" file="classify_test_16.test-02.out.dbed" />
57 <param name="only_valid" /> 62 <param name="only_valid" />
58 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" /> 63 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />
59 64
60 <output name="dr_disco_classify_output" file="classify_test_16.test-03.out.dbed" ftype="tabular" /> 65 <output name="dr_disco_classify_output" file="classify_test_16.test-03.out.dbed" ftype="tabular" />
61 </test> 66 </test>
67
62 <test> 68 <test>
63 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" /> 69 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
64 <param name="only_valid" /> 70 <param name="only_valid" />
65 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" /> 71 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />
66 72
79 <param name="only_valid" /> 85 <param name="only_valid" />
80 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" /> 86 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" />
81 87
82 <output name="dr_disco_classify_output" file="classify_test_16.test-06.out.dbed" /> 88 <output name="dr_disco_classify_output" file="classify_test_16.test-06.out.dbed" />
83 </test> 89 </test>
84
85 <test> 90 <test>
86 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" /> 91 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
87 <param name="only_valid" /> 92 <param name="only_valid" />
88 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" /> 93 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />
89 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" /> 94 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" />
96 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" /> 101 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />
97 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" /> 102 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" />
98 103
99 <output name="dr_disco_classify_output" file="classify_test_16.test-08.out.dbed" /> 104 <output name="dr_disco_classify_output" file="classify_test_16.test-08.out.dbed" />
100 </test> 105 </test>
106
101 </tests> 107 </tests>
102 108
103 <help><![CDATA[ 109 <help><![CDATA[
104 110
105 **What it does** 111 **What it does**
106 112
107 113 It filters fusion events that are likely to be true or false based on a variety of parameters provided in the input table.
108 114
109 **Attributions** 115 **Attributions**
110 116
111 This work is part of Youri Hoogstrate's PhD thesis. 117 This work is part of Youri Hoogstrate's PhD thesis.
112 118