annotate dunovo.xml @ 8:658eefb99fd7 draft

planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
author nick
date Fri, 12 Jan 2018 19:18:41 -0500
parents e7b88ffb8294
children fa563fa9b330
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
1 <?xml version="1.0"?>
8
658eefb99fd7 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents: 7
diff changeset
2 <tool id="dunovo" name="Du Novo: Make consensus reads" version="2.0.12">
0
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
3 <description>from duplex sequencing alignments</description>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
4 <requirements>
8
658eefb99fd7 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents: 7
diff changeset
5 <requirement type="package" version="2.0.12">dunovo</requirement>
0
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
6 <!-- TODO: require Python 2.7 -->
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
7 </requirements>
7
e7b88ffb8294 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents: 6
diff changeset
8 <version_command>make-consensi.py --version</version_command>
3
00dde366870a planemo upload for repository https://github.com/galaxyproject/dunovo commit b'a3ad9fbb3f010253808fc0c7329897a741ec9feb\n'
nick
parents: 2
diff changeset
9 <command detect_errors="exit_code">
7
e7b88ffb8294 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
nick
parents: 6
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'
0
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
11 #if $keep_sscs:
3
00dde366870a planemo upload for repository https://github.com/galaxyproject/dunovo commit b'a3ad9fbb3f010253808fc0c7329897a741ec9feb\n'
nick
parents: 2
diff changeset
12 --sscs1 '$sscs1' --sscs2 '$sscs2'
0
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
13 #end if
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
14 </command>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
15 <inputs>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
16 <param name="input" type="data" format="tabular" label="Aligned input reads" />
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\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."/>
4
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
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 &quot;N&quot; will be used."/>
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
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, &quot;N&quot; will be used."/>
0
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\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."/>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\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+">
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
22 <option value="sanger" selected="true">Sanger (PHRED 0 = &quot;!&quot;)</option>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
23 <option value="solexa">Solexa (PHRED 0 = &quot;@&quot;)</option>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
24 </param>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
25 <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences as well" />
4
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
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."/>
0
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
27 </inputs>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
28 <outputs>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
29 <data name="dcs1" format="fasta" label="$tool.name on $on_string (mate 1)"/>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
30 <data name="dcs2" format="fasta" label="$tool.name on $on_string (mate 2)"/>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
31 <data name="sscs1" format="fasta" label="$tool.name on $on_string (SSCS mate 1)">
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
32 <filter>keep_sscs</filter>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
33 </data>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
34 <data name="sscs2" format="fasta" label="$tool.name on $on_string (SSCS mate 2)">
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
35 <filter>keep_sscs</filter>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
36 </data>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
37 </outputs>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
38 <tests>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
39 <test>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
40 <param name="input" value="families.msa.tsv"/>
3
00dde366870a planemo upload for repository https://github.com/galaxyproject/dunovo commit b'a3ad9fbb3f010253808fc0c7329897a741ec9feb\n'
nick
parents: 2
diff changeset
41 <output name="dcs1" file="families.dcs_1.fa"/>
00dde366870a planemo upload for repository https://github.com/galaxyproject/dunovo commit b'a3ad9fbb3f010253808fc0c7329897a741ec9feb\n'
nick
parents: 2
diff changeset
42 <output name="dcs2" file="families.dcs_2.fa"/>
0
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
43 </test>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
44 </tests>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
45 <help>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
46
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
47 **What it does**
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
48
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\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.
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
50
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
51 -----
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
52
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
53 **Input**
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
54
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
55 This expects the output format of the "Align families" tool.
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
56
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
57 -----
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
58
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
59 **Output**
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
60
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\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.
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
62
4
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
63 </help>
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
64 <citations>
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
65 <citation type="bibtex">@article{Stoler2016,
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
66 author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
67 doi = {10.1186/s13059-016-1039-4},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
68 issn = {1474-760X},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
69 journal = {Genome biology},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
70 number = {1},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
71 pages = {180},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
72 pmid = {27566673},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
73 publisher = {Genome Biology},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
74 title = {{Streamlined analysis of duplex sequencing data with Du Novo.}},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
75 url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
76 volume = {17},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
77 year = {2016}
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
78 }</citation>
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
79 </citations>
0
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
80 </tool>