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comparison align_families.xml @ 6:9a0bee12b583 draft default tip

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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
children
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5:4bc49a5769ee 6:9a0bee12b583
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="align_families" name="Du Novo: Align families" version="0.5"> 2 <tool id="align_families" name="Du Novo: Align 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="7.221">mafft</requirement> 5 <requirement type="package" version="7.221">mafft</requirement>
6 <requirement type="package" version="0.5">duplex</requirement> 6 <requirement type="package" version="0.6">duplex</requirement>
7 <requirement type="set_environment">DUPLEX_DIR</requirement> 7 <requirement type="set_environment">DUPLEX_DIR</requirement>
8 <!-- TODO: require Python 2.7 --> 8 <!-- TODO: require Python 2.7 -->
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code">python \$DUPLEX_DIR/align_families.py -p \${GALAXY_SLOTS:-1} $input &gt; $output 10 <command detect_errors="exit_code">python "\$DUPLEX_DIR/align_families.py" -p \${GALAXY_SLOTS:-1} '$input' &gt; '$output'
11 </command> 11 </command>
12 <inputs> 12 <inputs>
13 <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/> 13 <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/>
14 </inputs> 14 </inputs>
15 <outputs> 15 <outputs>
23 <test> 23 <test>
24 <param name="input" value="families.in.tsv"/> 24 <param name="input" value="families.in.tsv"/>
25 <output name="output" file="families.sort.tsv"/> 25 <output name="output" file="families.sort.tsv"/>
26 </test> 26 </test>
27 </tests> 27 </tests>
28 <citations>
29 <citation type="bibtex">@article{Stoler2016,
30 author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},
31 doi = {10.1186/s13059-016-1039-4},
32 issn = {1474-760X},
33 journal = {Genome biology},
34 number = {1},
35 pages = {180},
36 pmid = {27566673},
37 publisher = {Genome Biology},
38 title = {{Streamlined analysis of duplex sequencing data with Du Novo.}},
39 url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673},
40 volume = {17},
41 year = {2016}
42 }</citation>
43 </citations>
28 <help> 44 <help>
29 45
30 **What it does** 46 **What it does**
31 47
32 This is for processing duplex sequencing data. It does a multiple sequence alignment on each (single-stranded) family of reads. 48 This is for processing duplex sequencing data. It does a multiple sequence alignment on each (single-stranded) family of reads.