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comparison make_families.xml @ 4:5fbeaa41b223 draft

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Update to Du Novo 2.0.6.
author nick
date Wed, 25 Oct 2017 19:26:43 -0400
parents 00dde366870a
children 000969829a5d
comparison
equal deleted inserted replaced
3:00dde366870a 4:5fbeaa41b223
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="make_families" name="Du Novo: Make families" version="0.8.1"> 2 <tool id="make_families" name="Du Novo: Make families" version="2.0.6">
3 <description>of duplex sequencing reads</description> 3 <description>of duplex sequencing reads</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="0.8.1">dunovo</requirement> 5 <requirement type="package" version="2.0.6">dunovo</requirement>
6 </requirements> 6 </requirements>
7 <!-- TODO: Add dependency on coreutils to get paste? --> 7 <!-- TODO: Add dependency on coreutils to get paste? -->
8 <command detect_errors="exit_code">make-families.sh -t $taglen -i $invariant '$fastq1' '$fastq2' &gt; '$output' 8 <command detect_errors="exit_code">make-families.sh -t $taglen -i $invariant '$fastq1' '$fastq2' &gt; '$output'
9 </command> 9 </command>
10 <inputs> 10 <inputs>
30 <param name="taglen" value="5"/> 30 <param name="taglen" value="5"/>
31 <param name="invariant" value="0"/> 31 <param name="invariant" value="0"/>
32 <output name="output" file="smoke.families.i0.tsv"/> 32 <output name="output" file="smoke.families.i0.tsv"/>
33 </test> 33 </test>
34 </tests> 34 </tests>
35 <citations>
36 <citation type="bibtex">@article{Stoler2016,
37 author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},
38 doi = {10.1186/s13059-016-1039-4},
39 issn = {1474-760X},
40 journal = {Genome biology},
41 number = {1},
42 pages = {180},
43 pmid = {27566673},
44 publisher = {Genome Biology},
45 title = {{Streamlined analysis of duplex sequencing data with Du Novo.}},
46 url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673},
47 volume = {17},
48 year = {2016}
49 }</citation>
50 </citations>
51 <help> 35 <help>
52 36
53 **What it does** 37 **What it does**
54 38
55 This tool is for processing raw duplex sequencing data, removing the barcodes and grouping by them into families of reads from the same fragment. 39 This tool is for processing raw duplex sequencing data, removing the barcodes and grouping by them into families of reads from the same fragment.
89 | ATG | CCT | ab | ATGCCT | 73 | ATG | CCT | ab | ATGCCT |
90 +-------+-------+-------+---------+ 74 +-------+-------+-------+---------+
91 | CCT | ATG | ba | ATGCCT | 75 | CCT | ATG | ba | ATGCCT |
92 +-------+-------+-------+---------+ 76 +-------+-------+-------+---------+
93 77
94 </help> 78 </help>
79 <citations>
80 <citation type="bibtex">@article{Stoler2016,
81 author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},
82 doi = {10.1186/s13059-016-1039-4},
83 issn = {1474-760X},
84 journal = {Genome biology},
85 number = {1},
86 pages = {180},
87 pmid = {27566673},
88 publisher = {Genome Biology},
89 title = {{Streamlined analysis of duplex sequencing data with Du Novo.}},
90 url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673},
91 volume = {17},
92 year = {2016}
93 }</citation>
94 </citations>
95 </tool> 95 </tool>