Mercurial > repos > erasmus-medical-center > dr_disco
changeset 2:173ca9768e22 draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit d29f5735b74a3919e6fc16c10435867ed4450576
| author | erasmus-medical-center |
|---|---|
| date | Fri, 28 Apr 2017 03:56:08 -0400 |
| parents | 9495360713d4 |
| children | 5348cfd3ba5c |
| files | dr-disco_bam-extract.xml dr-disco_detect.xml dr-disco_fix.xml macros.xml test-data/detect.txt test-data/fix_test-01.fixed.bam |
| diffstat | 6 files changed, 22 insertions(+), 9 deletions(-) [+] |
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--- a/dr-disco_bam-extract.xml Thu Mar 16 04:24:23 2017 -0400 +++ b/dr-disco_bam-extract.xml Fri Apr 28 03:56:08 2017 -0400 @@ -40,12 +40,15 @@ </test> </tests> - <help> -Extract reads from two chromosomal positions (and also takes mates with the same name) + <help><![CDATA[ + +**What it does** + +Extract reads that have their mate within one of two chromosomal positions (and also takes mates that correspond to these reads) Regions are in the format: chr1:123-546 - </help> + ]]></help> <expand macro="citations"/> </tool>
--- a/dr-disco_detect.xml Thu Mar 16 04:24:23 2017 -0400 +++ b/dr-disco_detect.xml Fri Apr 28 03:56:08 2017 -0400 @@ -34,7 +34,17 @@ </tests> <help><![CDATA[ - detects + +**What it does** + +Detects junctions in ('dr-disco fix' prepared) Chimeric alignments and tries to reconstruct fusion genes and genomic breakpoints using a Graph data structure. + +This software is in particular designed for RNA-Seq data prepared with random hexamer priming because of the presence of intronic reads. + +**Attributions** + +This work is part of Youri Hoogstrate's PhD thesis. + ]]></help> <expand macro="citations"/>
--- a/dr-disco_fix.xml Thu Mar 16 04:24:23 2017 -0400 +++ b/dr-disco_fix.xml Fri Apr 28 03:56:08 2017 -0400 @@ -29,7 +29,7 @@ **What it does** -Dr. Disco fix prepares chimeric alignment files produced by STAR for analysis with Dr. Disco (extract) and for visualization in genome browsers. +Dr. Disco fix prepares chimeric alignment files produced by STAR for analysis with Dr. Disco (detect) and for visualization in genome browsers. ]]></help> <expand macro="citations"/>
--- a/macros.xml Thu Mar 16 04:24:23 2017 -0400 +++ b/macros.xml Fri Apr 28 03:56:08 2017 -0400 @@ -1,12 +1,12 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="0.3.4">dr-disco</requirement> + <requirement type="package" version="0.6.0">dr-disco</requirement> <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">0.3.4</token> + <token name="@TOOL_VERSION@">0.6.0</token> <xml name="version_command"> <version_command>dr-disco --version | head -n 1</version_command>
--- a/test-data/detect.txt Thu Mar 16 04:24:23 2017 -0400 +++ b/test-data/detect.txt Fri Apr 28 03:56:08 2017 -0400 @@ -1,2 +1,2 @@ -chr-A pos-A direction-A chr-B pos-B direction-B filter-status intronic/exonic score soft+hardclips n-split-reads n-discordant-reads n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges data-structure -chr21 39877811 - chr21 42873374 + n_discordant_reads=0<1,n_support=3<8 intronic 9 6 3 0 1 1 1 0 0 1.0 1.0 chr21:39877811/39877812(-)->chr21:42873374/42873375(+):(spanning_paired_1_t:3,spanning_paired_2_t:3) +chr-A pos-A direction-A chr-B pos-B direction-B genomic-distance filter-status circRNA intronic/exonic score soft+hardclips n-split-reads n-discordant-reads n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges bp-pos-stddev entropy-disco-bps data-structure +chr21 39877811 - chr21 42873374 + 2995563 n_discordant_reads=0<1,n_support=3<8 linear intronic 9 6 3 0 1 1 1 0 0 1.0000 1.0000 0.0000 0.0000 chr21:39877811/39877812(-)->chr21:42873374/42873375(+):(spanning_paired_1_t:3,spanning_paired_2_t:3)