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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
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5:4bc49a5769ee 6:9a0bee12b583
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="duplex" name="Du Novo: Make consensus reads" version="0.5"> 2 <tool id="duplex" name="Du Novo: Make consensus reads" version="0.6">
3 <description>from duplex sequencing alignments</description> 3 <description>from duplex sequencing alignments</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 <!-- TODO: require Python 2.7 --> 7 <!-- TODO: require Python 2.7 -->
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 python \$DUPLEX_DIR/dunovo.py -r $min_reads -q $qual_thres -F $qual_format $input 10 python "\$DUPLEX_DIR/dunovo.py" -r $min_reads -q $qual_thres -F $qual_format '$input'
11 #if $keep_sscs: 11 #if $keep_sscs:
12 --sscs-file sscs.fa 12 --sscs-file sscs.fa
13 #end if 13 #end if
14 > duplex.fa 14 > duplex.fa
15 && python \$DUPLEX_DIR/utils/outconv.py duplex.fa -1 $dcs1 -2 $dcs2 15 && python "\$DUPLEX_DIR/utils/outconv.py" duplex.fa -1 '$dcs1' -2 '$dcs2'
16 #if $keep_sscs: 16 #if $keep_sscs:
17 && python \$DUPLEX_DIR/utils/outconv.py sscs.fa -1 $sscs1 -2 $sscs2 17 && python "\$DUPLEX_DIR/utils/outconv.py" sscs.fa -1 '$sscs1' -2 '$sscs2'
18 #end if 18 #end if
19 ]]> 19 ]]>
20 </command> 20 </command>
21 <inputs> 21 <inputs>
22 <param name="input" type="data" format="tabular" label="Aligned input reads" /> 22 <param name="input" type="data" format="tabular" label="Aligned input reads" />
43 <param name="input" value="families.msa.tsv"/> 43 <param name="input" value="families.msa.tsv"/>
44 <output name="dcs1" file="families.cons_1.fa"/> 44 <output name="dcs1" file="families.cons_1.fa"/>
45 <output name="dcs2" file="families.cons_2.fa"/> 45 <output name="dcs2" file="families.cons_2.fa"/>
46 </test> 46 </test>
47 </tests> 47 </tests>
48 <citations>
49 <citation type="bibtex">@article{Stoler2016,
50 author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},
51 doi = {10.1186/s13059-016-1039-4},
52 issn = {1474-760X},
53 journal = {Genome biology},
54 number = {1},
55 pages = {180},
56 pmid = {27566673},
57 publisher = {Genome Biology},
58 title = {{Streamlined analysis of duplex sequencing data with Du Novo.}},
59 url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673},
60 volume = {17},
61 year = {2016}
62 }</citation>
63 </citations>
48 <help> 64 <help>
49 65
50 **What it does** 66 **What it does**
51 67
52 This is for processing duplex sequencing data. It creates single-strand and duplex consensus reads from aligned read families. 68 This is for processing duplex sequencing data. It creates single-strand and duplex consensus reads from aligned read families.