Mercurial > repos > nick > dunovo
annotate dunovo.xml @ 21:f509cd1d5a78 draft
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fd1625359a101d8a6b0b8d97028cc8be509398f2\n'-dirty
author | nick |
---|---|
date | Thu, 04 Jan 2018 23:55:06 -0500 |
parents | 78542cc82cb6 |
children | db602e459536 |
rev | line source |
---|---|
20
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
1 <?xml version="1.0"?> |
21
f509cd1d5a78
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fd1625359a101d8a6b0b8d97028cc8be509398f2\n'-dirty
nick
parents:
20
diff
changeset
|
2 <tool id="dunovo" name="Du Novo: Make consensus reads" version="2.0.10"> |
20
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
3 <description>from duplex sequencing alignments</description> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
4 <requirements> |
21
f509cd1d5a78
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fd1625359a101d8a6b0b8d97028cc8be509398f2\n'-dirty
nick
parents:
20
diff
changeset
|
5 <requirement type="package" version="2.0.10">dunovo</requirement> |
20
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
6 <!-- TODO: require Python 2.7 --> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
7 </requirements> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
8 <version_command>make-consensi.py --version</version_command> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
9 <command detect_errors="exit_code"> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
10 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' |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
11 #if $keep_sscs: |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
12 --sscs1 '$sscs1' --sscs2 '$sscs2' |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
13 #end if |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
14 </command> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
15 <inputs> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
16 <param name="input" type="data" format="tabular" label="Aligned input reads" /> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
17 <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
18 <param name="cons_thres" type="float" value="0.5" min="0.5" max="1.0" label="Consensus % threshold" help="The consensus base must be present in more than this fraction of the reads, or "N" will be used."/> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
19 <param name="min_cons_reads" type="integer" value="0" min="0" label="Minimum number of reads for a consensus base." help="If no base at the position appears in at least this many reads, "N" will be used."/> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
20 <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
21 <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+"> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
22 <option value="sanger" selected="true">Sanger (PHRED 0 = "!")</option> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
23 <option value="solexa">Solexa (PHRED 0 = "@")</option> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
24 </param> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
25 <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences as well" /> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
26 <param name="phone" type="boolean" truevalue="--phone-home" falsevalue="" checked="False" label="Send usage data" help="Report helpful usage data to the developer, to better understand the use cases and performance of the tool. The only data which will be recorded is the name and version of the tool, the size of the input data, the number of processes used, the time and memory taken to process it, and the IP address of the machine running it. Also, if the tool fails, it will report the name of the exception thrown and the line of code it occurred in. The parameters and input/output dataset names are not sent. All the reporting and recording code is available at https://github.com/NickSto/ET."/> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
27 </inputs> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
28 <outputs> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
29 <data name="dcs1" format="fasta" label="$tool.name on $on_string (mate 1)"/> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
30 <data name="dcs2" format="fasta" label="$tool.name on $on_string (mate 2)"/> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
31 <data name="sscs1" format="fasta" label="$tool.name on $on_string (SSCS mate 1)"> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
32 <filter>keep_sscs</filter> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
33 </data> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
34 <data name="sscs2" format="fasta" label="$tool.name on $on_string (SSCS mate 2)"> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
35 <filter>keep_sscs</filter> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
36 </data> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
37 </outputs> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
38 <tests> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
39 <test> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
40 <param name="input" value="families.msa.tsv"/> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
41 <output name="dcs1" file="families.dcs_1.fa"/> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
42 <output name="dcs2" file="families.dcs_2.fa"/> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
43 </test> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
44 </tests> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
45 <help> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
46 |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
47 **What it does** |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
48 |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
49 This is for processing duplex sequencing data. It creates single-strand and duplex consensus reads from aligned read families. |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
50 |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
51 ----- |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
52 |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
53 **Input** |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
54 |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
55 This expects the output format of the "Align families" tool. |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
56 |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
57 ----- |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
58 |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
59 **Output** |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
60 |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
61 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. |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
62 |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
63 </help> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
64 <citations> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
65 <citation type="bibtex">@article{Stoler2016, |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
66 author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton}, |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
67 doi = {10.1186/s13059-016-1039-4}, |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
68 issn = {1474-760X}, |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
69 journal = {Genome biology}, |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
70 number = {1}, |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
71 pages = {180}, |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
72 pmid = {27566673}, |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
73 publisher = {Genome Biology}, |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
74 title = {{Streamlined analysis of duplex sequencing data with Du Novo.}}, |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
75 url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673}, |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
76 volume = {17}, |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
77 year = {2016} |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
78 }</citation> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
79 </citations> |
78542cc82cb6
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents:
diff
changeset
|
80 </tool> |