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comparison lordec_graph.xml @ 4:f0b144292846 draft

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author abretaud
date Wed, 31 Aug 2016 11:22:26 -0400
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3:e978c66bb55f 4:f0b144292846
1 <tool id="lordecgraph" name="lordec_graph" version="0.5.3"> 1 <tool id="lordecgraph" name="lordec_graph" version="0.6">
2 <description>is an efficient tool to generate de Bruijn graph from PacBio corrected reads</description> 2 <description>is an efficient tool to generate de Bruijn graph from PacBio corrected reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.5.3">lordec</requirement> 4 <requirement type="package" version="0.6">lordec</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command><![CDATA[
7 lordec-build-SR-graph 7 lordec-build-SR-graph
8 -2 $short_reads 8 -2 $short_reads
9 -k $kmer_len 9 -k $kmer_len
10 -s $solid_threshold 10 -s $solid_threshold
11 -g $outgraph 11 -g $outgraph
12 #if str( $advanced_options.advanced_options_selector) == "advanced" 12 #if str( $advanced_options.advanced_options_selector) == "advanced"
13 -T $advanced_options.threads 13 -T $advanced_options.threads
14 #end if 14 #end if
15 2&gt;1 15 2>&1
16 ]]>
16 </command> 17 </command>
17 18
18 <inputs> 19 <inputs>
19 <!-- Input data files --> 20 <!-- Input data files -->
20 <param name="short_reads" type="data" format="fasta,fastq.gz,fastq" label="short read FASTA/Q file" /> 21 <param name="short_reads" type="data" format="fasta,fastq.gz,fastq" label="short read FASTA/Q file" />
53 54
54 ------- 55 -------
55 56
56 **Integrated by** 57 **Integrated by**
57 58
58 Yvan Le Bras and Cyril Monjeaud 59 Yvan Le Bras and Cyril Monjeaud
59 60
60 GenOuest Bio-informatics Core Facility 61 GenOuest Bio-informatics Core Facility
61 62
62 UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France) 63 UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France)
63 64
67 68
68 `Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. &lt;https://www.e-biogenouest.org/resources/128&gt;`_ 69 `Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. &lt;https://www.e-biogenouest.org/resources/128&gt;`_
69 70
70 </help> 71 </help>
71 <citations> 72 <citations>
73 <citation type="doi">10.1186/s13742-015-0105-2</citation>
72 <citation type="doi">10.1093/bioinformatics/btu538</citation> 74 <citation type="doi">10.1093/bioinformatics/btu538</citation>
73 <citation type="bibtex">@INPROCEEDINGS{JOBIM2013, 75 <citation type="bibtex">@INPROCEEDINGS{JOBIM2013,
74 author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.}, 76 author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.},
75 title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France}, 77 title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France},
76 booktitle = {JOBIM 2013 Proceedings}, 78 booktitle = {JOBIM 2013 Proceedings},
77 year = {2013}, 79 year = {2013},
78 url = {https://www.e-biogenouest.org/resources/128}, 80 url = {https://www.e-biogenouest.org/resources/128},
79 pages = {97-106} 81 pages = {97-106}
80 }</citation> 82 }</citation>
81 </citations> 83 </citations>
82 </tool> 84 </tool>