Mercurial > repos > erasmus-medical-center > dr_disco

annotate dr-disco_classify.xml @ 11:3743fd602fa9 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 183cebdfe3a34204fd8aa1c6dce6bf6514b94c2d
author erasmus-medical-center
date Fri, 03 Nov 2017 07:23:57 -0400
parents f2c70d589596
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
922b52cf9b35 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b4991fb40364a975d0ea782035b930874c57665c
erasmus-medical-center
parents: 3
diff changeset
1 <tool id="dr_disco_classify" name="Dr. Disco (classify)" version="@TOOL_VERSION@">
3
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
2 <description>Classifies detected break-points in RNA-seq based on corresponding statistics and blacklists</description>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
3
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
4 <macros>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
5 <import>macros.xml</import>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
6 </macros>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
7
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
8 <expand macro="requirements"/>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
9 <expand macro="version_command"/>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
10
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
12 dr-disco
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
13 classify
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
14
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
15 ${only_valid}
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
16
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
17 #if $blacklist_regions:
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
18 --blacklist-regions '${blacklist_regions}'
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
19 #end if
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
20
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
21 #if $blacklist_junctions:
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
22 --blacklist-junctions '${blacklist_junctions}'
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
23 #end if
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
24
10
f2c70d589596 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 3b03a60c8a46cc23f6fbbb9e32111b39c6044fad
erasmus-medical-center
parents: 8
diff changeset
25 --min-chim-overhang '${min_chim_overhang}'
f2c70d589596 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 3b03a60c8a46cc23f6fbbb9e32111b39c6044fad
erasmus-medical-center
parents: 8
diff changeset
26
3
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
27 '${dr_disco_detect_output}'
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
28 '${dr_disco_classify_output}'
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
29 ]]></command>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
30
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
31 <inputs>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
32 <param name="dr_disco_detect_output" type="data" format="tabular" label="Output of Dr. Disco Detect" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
33 <param name="only_valid" argument="--only-valid" truevalue="--only-valid" falsevalue="" type="boolean" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
34
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
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/)" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
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/)" />
10
f2c70d589596 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 3b03a60c8a46cc23f6fbbb9e32111b39c6044fad
erasmus-medical-center
parents: 8
diff changeset
37
f2c70d589596 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 3b03a60c8a46cc23f6fbbb9e32111b39c6044fad
erasmus-medical-center
parents: 8
diff changeset
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" />
3
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
39 </inputs>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
40
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
41 <outputs>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
42 <data name="dr_disco_classify_output" format="tabular" label="${tool.name} on ${dr_disco_detect_output.name}" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
43 </outputs>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
44
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
45 <tests>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
46 <test>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
47 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
48 <param name="only_valid" value="" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
49
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
50 <output name="dr_disco_classify_output" file="classify_test_16.test-01.out.dbed" ftype="tabular" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
51 </test>
10
f2c70d589596 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 3b03a60c8a46cc23f6fbbb9e32111b39c6044fad
erasmus-medical-center
parents: 8
diff changeset
52
3
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
53 <test>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
54 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
55 <param name="only_valid" value="--only-valid" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
56
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
57 <output name="dr_disco_classify_output" file="classify_test_16.test-02.out.dbed" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
58 </test>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
59
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
60 <test>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
61 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
62 <param name="only_valid" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
63 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
64
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
65 <output name="dr_disco_classify_output" file="classify_test_16.test-03.out.dbed" ftype="tabular" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
66 </test>
10
f2c70d589596 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 3b03a60c8a46cc23f6fbbb9e32111b39c6044fad
erasmus-medical-center
parents: 8
diff changeset
67
3
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
68 <test>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
69 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
70 <param name="only_valid" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
71 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
72
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
73 <output name="dr_disco_classify_output" file="classify_test_16.test-04.out.dbed" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
74 </test>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
75
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
76 <test>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
77 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
78 <param name="only_valid" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
79 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
80
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
81 <output name="dr_disco_classify_output" file="classify_test_16.test-05.out.dbed" ftype="tabular" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
82 </test>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
83 <test>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
84 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
85 <param name="only_valid" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
86 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
87
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
88 <output name="dr_disco_classify_output" file="classify_test_16.test-06.out.dbed" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
89 </test>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
90 <test>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
91 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
92 <param name="only_valid" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
93 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
94 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
95
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
96 <output name="dr_disco_classify_output" file="classify_test_16.test-07.out.dbed" ftype="tabular" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
97 </test>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
98 <test>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
99 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
100 <param name="only_valid" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
101 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
102 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
103
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
104 <output name="dr_disco_classify_output" file="classify_test_16.test-08.out.dbed" />
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
105 </test>
10
f2c70d589596 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 3b03a60c8a46cc23f6fbbb9e32111b39c6044fad
erasmus-medical-center
parents: 8
diff changeset
106
3
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
107 </tests>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
108
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
109 <help><![CDATA[
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
110
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
111 **What it does**
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
112
11
3743fd602fa9 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 183cebdfe3a34204fd8aa1c6dce6bf6514b94c2d
erasmus-medical-center
parents: 10
diff changeset
113 * Step 3 in dr-disco pipeline
3
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
114
11
3743fd602fa9 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 183cebdfe3a34204fd8aa1c6dce6bf6514b94c2d
erasmus-medical-center
parents: 10
diff changeset
115 This tools filters the detected junctions which are likely to be true or false based on a variety of parameters provided in the input table. This filtering is in particular based on variables derived from the shape of the alignment and the ratio of split and spanning reads.
3743fd602fa9 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 183cebdfe3a34204fd8aa1c6dce6bf6514b94c2d
erasmus-medical-center
parents: 10
diff changeset
116
3743fd602fa9 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 183cebdfe3a34204fd8aa1c6dce6bf6514b94c2d
erasmus-medical-center
parents: 10
diff changeset
117 **Attribution**
3
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
118
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
119 This work is part of Youri Hoogstrate's PhD thesis.
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
120
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
121 ]]></help>
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
122
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents:
diff changeset
123 <expand macro="citations"/>
11
3743fd602fa9 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 183cebdfe3a34204fd8aa1c6dce6bf6514b94c2d
erasmus-medical-center
parents: 10
diff changeset
124 </tool>