Mercurial > repos > yating-l > regtools_junctions_extract

annotate README.rst @ 1:06d9062f5430 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 93217f9e3a1bc1afc8ce971176e4ae0169a8f265
author sargentl
date Wed, 28 Nov 2018 14:20:39 -0500
parents 01ed8e112f2a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
1 A Galaxy Wrapper for regtools
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
2 =============================
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
3
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
4 This is a modified Galaxy wrapper for regtools which is based on the previous wrapper written by Remi Marenco (https://github.com/remimarenco/regtools). "regtools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context" (https://regtools.readthedocs.io/en/latest/).
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
5
1
06d9062f5430 planemo upload commit 93217f9e3a1bc1afc8ce971176e4ae0169a8f265
sargentl
parents: 0
diff changeset
6 This wrapper adds an validation step to check if the output files are valid BED format. The lines with invalid strand (neither "+" or "-") will be removed.
0
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
7
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
8 This wrapper creates a new 13th column to store the scores. The scores in column 4 will be changed to 1000.
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
9
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
10 The output is BED 12+1.