Mercurial > repos > crs4 > sequel
comparison sequel_wrapper.xml @ 2:208ce57f9221 draft default tip
Fix version for blat requirement (reported by Bjoern Gruening). Upgrade BWA dependency to v. 0.7.7 . Update Orione citation.
author | crs4 |
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date | Fri, 18 Jul 2014 09:19:43 -0400 |
parents | ccadfae70b02 |
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1:ccadfae70b02 | 2:208ce57f9221 |
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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> |