# 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} - } - -