Mercurial > repos > nick > duplex

comparison make_families.xml @ 6:9a0bee12b583 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 b'9fbe4b8871038d2945fa4b9ee0b5f89cf4e4f494\n'-dirty
author nick
date Mon, 06 Feb 2017 23:39:11 -0500
parents 4bc49a5769ee
children
comparison
equal deleted inserted replaced
5:4bc49a5769ee 6:9a0bee12b583
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="make_families" name="Du Novo: Make families" version="0.5"> 2 <tool id="make_families" name="Du Novo: Make families" version="0.6">
3 <description>of duplex sequencing reads</description> 3 <description>of duplex sequencing reads</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="0.5">duplex</requirement> 5 <requirement type="package" version="0.6">duplex</requirement>
6 <requirement type="set_environment">DUPLEX_DIR</requirement> 6 <requirement type="set_environment">DUPLEX_DIR</requirement>
7 </requirements> 7 </requirements>
8 <!-- TODO: Add dependency on coreutils to get paste? --> 8 <!-- TODO: Add dependency on coreutils to get paste? -->
9 <command>paste $fastq1 $fastq2 9 <command>paste '$fastq1' '$fastq2'
10 | paste - - - - 10 | paste - - - -
11 | awk -f \$DUPLEX_DIR/make-barcodes.awk -v TAG_LEN=$taglen -v INVARIANT=$invariant 11 | awk -f "\$DUPLEX_DIR/make-barcodes.awk" -v TAG_LEN=$taglen -v INVARIANT=$invariant
12 | sort 12 | sort
13 &gt; $output 13 &gt; '$output'
14 </command> 14 </command>
15 <inputs> 15 <inputs>
16 <param name="fastq1" type="data" format="fastq" label="Sequencing reads, mate 1"/> 16 <param name="fastq1" type="data" format="fastq" label="Sequencing reads, mate 1"/>
17 <param name="fastq2" type="data" format="fastq" label="Sequencing reads, mate 2"/> 17 <param name="fastq2" type="data" format="fastq" label="Sequencing reads, mate 2"/>
18 <param name="taglen" type="integer" value="12" min="0" label="Tag length" help="length of each random barcode on the ends of the fragments"/> 18 <param name="taglen" type="integer" value="12" min="0" label="Tag length" help="length of each random barcode on the ends of the fragments"/>
35 <param name="taglen" value="5"/> 35 <param name="taglen" value="5"/>
36 <param name="invariant" value="0"/> 36 <param name="invariant" value="0"/>
37 <output name="output" file="smoke.families.i0.tsv"/> 37 <output name="output" file="smoke.families.i0.tsv"/>
38 </test> 38 </test>
39 </tests> 39 </tests>
40 <citations>
41 <citation type="bibtex">@article{Stoler2016,
42 author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},
43 doi = {10.1186/s13059-016-1039-4},
44 issn = {1474-760X},
45 journal = {Genome biology},
46 number = {1},
47 pages = {180},
48 pmid = {27566673},
49 publisher = {Genome Biology},
50 title = {{Streamlined analysis of duplex sequencing data with Du Novo.}},
51 url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673},
52 volume = {17},
53 year = {2016}
54 }</citation>
55 </citations>
40 <help> 56 <help>
41 57
42 **What it does** 58 **What it does**
43 59
44 This tool is for processing raw duplex sequencing data, removing the barcodes and grouping by them into families of reads from the same fragment. 60 This tool is for processing raw duplex sequencing data, removing the barcodes and grouping by them into families of reads from the same fragment.