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comparison lordec_trim.xml @ 6:d135caa42d04 draft

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author abretaud
date Wed, 31 Aug 2016 11:22:43 -0400
parents 46caddb8b8eb
children 2978f45ed09f
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5:86ac3b90e9f6 6:d135caa42d04
1 <tool id="lordectrim" name="lordectrim" version="0.5.3"> 1 <tool id="lordectrim" name="lordectrim" version="0.5.3.1">
2 <description>is an efficient tool to trim weak regions of PacBio corrected reads</description> 2 <description>is an efficient tool to trim weak regions of 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 #if $split 7 #if $split
8 lordec-trim-split 8 lordec-trim-split
9 #else 9 #else
10 lordec-trim 10 lordec-trim
11 #end if 11 #end if
12 -i $long_reads 12 -i $long_reads
13 -o $corrected_read_file 13 -o $corrected_read_file
14 ]]>
14 </command> 15 </command>
15 16
16 <inputs> 17 <inputs>
17 <!-- Input data files --> 18 <!-- Input data files -->
18 <param name="long_reads" type="data" format="fasta,fastq.gz,fastq" label="long read FASTA/Q file" help="PacBio reads files" /> 19 <param name="long_reads" type="data" format="fasta,fastq.gz,fastq" label="long read FASTA/Q file" help="PacBio reads files" />
37 38
38 ------- 39 -------
39 40
40 **Integrated by** 41 **Integrated by**
41 42
42 Yvan Le Bras and Cyril Monjeaud 43 Yvan Le Bras and Cyril Monjeaud
43 44
44 GenOuest Bio-informatics Core Facility 45 GenOuest Bio-informatics Core Facility
45 46
46 UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France) 47 UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France)
47 48
51 52
52 `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;`_ 53 `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;`_
53 54
54 </help> 55 </help>
55 <citations> 56 <citations>
57 <citation type="doi">10.1186/s13742-015-0105-2</citation>
56 <citation type="doi">10.1093/bioinformatics/btu538</citation> 58 <citation type="doi">10.1093/bioinformatics/btu538</citation>
57 <citation type="bibtex">@INPROCEEDINGS{JOBIM2013, 59 <citation type="bibtex">@INPROCEEDINGS{JOBIM2013,
58 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.}, 60 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.},
59 title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France}, 61 title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France},
60 booktitle = {JOBIM 2013 Proceedings}, 62 booktitle = {JOBIM 2013 Proceedings},
61 year = {2013}, 63 year = {2013},
62 url = {https://www.e-biogenouest.org/resources/128}, 64 url = {https://www.e-biogenouest.org/resources/128},
63 pages = {97-106} 65 pages = {97-106}
64 }</citation> 66 }</citation>
65 </citations> 67 </citations>
66 </tool> 68 </tool>