Mercurial > repos > nick > dunovo

annotate precheck.xml @ 11:0f8e0dc73d1d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
author nick
date Wed, 16 Feb 2022 22:59:00 +0000
parents 9dc43bf7d1db
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
1 <?xml version="1.0"?>
11
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents: 10
diff changeset
2 <tool id="precheck" name="Du Novo: Check input" version="3.0.2">
9
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
3 <requirements>
11
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents: 10
diff changeset
4 <requirement type="package" version="3.0.2">dunovo</requirement>
9
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
5 </requirements>
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
6 <description>for family content</description>
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
7 <command detect_errors="exit_code">
10
9dc43bf7d1db planemo upload for repository https://github.com/galaxyproject/dunovo commit b'230f018da2c0bc4eedc72e0f70eac0df1e85ebdb\n'-dirty
nick
parents: 9
diff changeset
8 precheck.py $check_ids --tag-length $tag_len --constant-length $const_len --min-reads $min_reads
9dc43bf7d1db planemo upload for repository https://github.com/galaxyproject/dunovo commit b'230f018da2c0bc4eedc72e0f70eac0df1e85ebdb\n'-dirty
nick
parents: 9
diff changeset
9 '$fastq1' '$fastq2' &gt; '$output'
9
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
10 </command>
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
11 <inputs>
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
12 <param name="fastq1" type="data" format="fastq" label="Sequencing reads, mate 1"/>
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
13 <param name="fastq2" type="data" format="fastq" label="Sequencing reads, mate 2"/>
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
14 <param name="min_reads" type="integer" value="3" min="0" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/>
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
15 <param name="tag_len" type="integer" value="12" min="0" label="Tag length" help="Length of each random barcode on the ends of the fragments."/>
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
16 <param name="const_len" type="integer" value="5" min="0" label="Invariant sequence length" help="Length of the sequence between the tag and actual sample sequence (the restriction site, normally)."/>
10
9dc43bf7d1db planemo upload for repository https://github.com/galaxyproject/dunovo commit b'230f018da2c0bc4eedc72e0f70eac0df1e85ebdb\n'-dirty
nick
parents: 9
diff changeset
17 <param name="check_ids" type="boolean" truevalue="--validate" falsevalue="--no-check-ids" checked="True" label="Check read names" help="Make sure the ids of the reads in each pair is the same. If checked, this will fail if there is a mismatch."/>
9
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
18 </inputs>
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
19 <outputs>
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
20 <data name="output" format="tabular"/>
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
21 </outputs>
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
22
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
23 <help>
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
24
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
25 .. class:: infomark
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
26
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
27 **What it does**
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
28
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
29 This tool lets you check your input reads before running the Du Novo pipeline. It will tell you about how many unique barcodes are in your dataset, how many families have boths strands present, how many consensus sequences of each type it will be able to form, and more.
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
30
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
31 .. class:: infomark
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
32
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
33 **Input**
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
34
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
35 The input must be in FASTQ format.
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
36
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
37 </help>
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
38
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
39 <citations>
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
40 <citation type="bibtex">@article{Stoler2016,
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
41 author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
42 doi = {10.1186/s13059-016-1039-4},
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
43 issn = {1474-760X},
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
44 journal = {Genome biology},
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
45 number = {1},
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
46 pages = {180},
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
47 pmid = {27566673},
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
48 publisher = {Genome Biology},
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
49 title = {{Streamlined analysis of duplex sequencing data with Du Novo.}},
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
50 url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673},
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
51 volume = {17},
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
52 year = {2016}
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
53 }</citation>
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
54 </citations>
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
55
fa563fa9b330 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
nick
parents:
diff changeset
56 </tool>