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Fix version for blat requirement (reported by Bjoern Gruening). Upgrade BWA dependency to v. 0.7.7 . Update Orione citation.
author crs4
date Fri, 18 Jul 2014 09:19:43 -0400
parents ccadfae70b02
children
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1:ccadfae70b02 2:208ce57f9221
1 <tool id="sequel_wrapper" name="SEQuel" version="0.2"> 1 <tool id="sequel_wrapper" name="SEQuel" version="0.2">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.6.2">bwa</requirement> 4 <requirement type="package" version="0.7.7">bwa</requirement>
5 <requirement type="package" version="35">blat</requirement> 5 <requirement type="package" version="35x1">blat</requirement>
6 <requirement type="package" version="1.0.2">sequel</requirement> 6 <requirement type="package" version="1.0.2">sequel</requirement>
7 </requirements> 7 </requirements>
8 <command interpreter="python"> 8 <command interpreter="python">
9 sequel_wrapper.py -t \${GALAXY_SLOTS:-8} -p \${GALAXY_SLOTS:-8} -u 1 9 sequel_wrapper.py -t \${GALAXY_SLOTS:-8} -p \${GALAXY_SLOTS:-8} -u 1
10 --sequel_jar_path=\$SEQUEL_JAR_PATH --read1=$read1 --read2=$read2 --contigs=$contigs 10 --sequel_jar_path=\$SEQUEL_JAR_PATH --read1=$read1 --read2=$read2 --contigs=$contigs
110 110
111 During the pre-processing stage, a SAM file per contig is created. Due to runtime considerations, these files are kept open simultaneously. The program will crash when the number of contigs in the assembly is too high. 111 During the pre-processing stage, a SAM file per contig is created. Due to runtime considerations, these files are kept open simultaneously. The program will crash when the number of contigs in the assembly is too high.
112 112
113 **License and citation** 113 **License and citation**
114 114
115 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_. 115 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
116 116
117 .. _CRS4 Srl.: http://www.crs4.it/ 117 .. _CRS4 Srl.: http://www.crs4.it/
118 .. _MIT license: http://opensource.org/licenses/MIT 118 .. _MIT license: http://opensource.org/licenses/MIT
119 119
120 If you use this tool in Galaxy, please cite |Cuccuru2013|_. 120 You can use this tool only if you agree to the license terms of: `SEQuel`_.
121
122 .. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, accepted
123 .. _Cuccuru2013: http://orione.crs4.it/
124
125 This tool uses `SEQuel`_, which is licensed separately. Please cite |Ronen2012|_.
126 121
127 .. _SEQuel: http://bix.ucsd.edu/SEQuel/ 122 .. _SEQuel: http://bix.ucsd.edu/SEQuel/
123
124 If you use this tool, please cite:
125
126 - |Cuccuru2014|_
127 - |Ronen2012|_.
128
129 .. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
130 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
128 .. |Ronen2012| replace:: Ronen R., *et al.* (2012) SEQuel: improving the accuracy of genome assemblies. *Bioinformatics* 28 (12), i188-i196 131 .. |Ronen2012| replace:: Ronen R., *et al.* (2012) SEQuel: improving the accuracy of genome assemblies. *Bioinformatics* 28 (12), i188-i196
129 .. _Ronen2012: http://bioinformatics.oxfordjournals.org/content/28/12/i188 132 .. _Ronen2012: http://bioinformatics.oxfordjournals.org/content/28/12/i188
130 </help> 133 </help>
131 </tool> 134 </tool>