# HG changeset patch
# User nick
# Date 1510324251 18000
# Node ID 78542cc82cb64236dc578ba840796a49fd6d8766
# Parent e5d1d90c099bc85a64f72cb368339acf7db2b14d
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
diff -r e5d1d90c099b -r 78542cc82cb6 dunovo.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/dunovo.xml Fri Nov 10 09:30:51 2017 -0500
@@ -0,0 +1,80 @@
+
+
+ from duplex sequencing alignments
+
+ dunovo
+
+
+ make-consensi.py --version
+
+ make-consensi.py --galaxy $phone --processes \${GALAXY_SLOTS:-1} --min-reads $min_reads --qual $qual_thres --qual-format $qual_format --cons-thres $cons_thres --min-cons-reads $min_cons_reads '$input' --dcs1 '$dcs1' --dcs2 '$dcs2'
+ #if $keep_sscs:
+ --sscs1 '$sscs1' --sscs2 '$sscs2'
+ #end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ keep_sscs
+
+
+ keep_sscs
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+This is for processing duplex sequencing data. It creates single-strand and duplex consensus reads from aligned read families.
+
+-----
+
+**Input**
+
+This expects the output format of the "Align families" tool.
+
+-----
+
+**Output**
+
+This will output final, duplex consensus reads in two FASTA files (first and second reads in the pairs). Optionally, you can save the single-strand reads too, in a separate FASTA file.
+
+
+
+ @article{Stoler2016,
+ author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},
+ doi = {10.1186/s13059-016-1039-4},
+ issn = {1474-760X},
+ journal = {Genome biology},
+ number = {1},
+ pages = {180},
+ pmid = {27566673},
+ publisher = {Genome Biology},
+ title = {{Streamlined analysis of duplex sequencing data with Du Novo.}},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673},
+ volume = {17},
+ year = {2016}
+ }
+
+
diff -r e5d1d90c099b -r 78542cc82cb6 make_consensi.xml
--- a/make_consensi.xml Fri Nov 10 08:50:09 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,80 +0,0 @@
-
-
- from duplex sequencing alignments
-
- dunovo
-
-
- make-consensi.py --version
-
- make-consensi.py --galaxy $phone --processes \${GALAXY_SLOTS:-1} --min-reads $min_reads --qual $qual_thres --qual-format $qual_format --cons-thres $cons_thres --min-cons-reads $min_cons_reads '$input' --dcs1 '$dcs1' --dcs2 '$dcs2'
- #if $keep_sscs:
- --sscs1 '$sscs1' --sscs2 '$sscs2'
- #end if
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- keep_sscs
-
-
- keep_sscs
-
-
-
-
-
-
-
-
-
-
-
-**What it does**
-
-This is for processing duplex sequencing data. It creates single-strand and duplex consensus reads from aligned read families.
-
------
-
-**Input**
-
-This expects the output format of the "Align families" tool.
-
------
-
-**Output**
-
-This will output final, duplex consensus reads in two FASTA files (first and second reads in the pairs). Optionally, you can save the single-strand reads too, in a separate FASTA file.
-
-
-
- @article{Stoler2016,
- author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},
- doi = {10.1186/s13059-016-1039-4},
- issn = {1474-760X},
- journal = {Genome biology},
- number = {1},
- pages = {180},
- pmid = {27566673},
- publisher = {Genome Biology},
- title = {{Streamlined analysis of duplex sequencing data with Du Novo.}},
- url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673},
- volume = {17},
- year = {2016}
- }
-
-