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Update Orione citation. Update dependency to SSPACE Basic v2.1 . Add <citations>.
author crs4
date Mon, 27 Oct 2014 14:11:57 -0400
parents 93fa7ecb5292
children b3a6b51c44e0
comparison
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1:93fa7ecb5292 2:bc4451edb703
1 <tool id="sspace" name="SSPACE" version="1.0.6"> 1 <tool id="sspace" name="SSPACE" version="1.0.7">
2 <description>scaffolder</description> 2 <description>scaffolder</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.0">sspace</requirement> 4 <requirement type="package" version="2.1">sspace</requirement>
5 </requirements> 5 </requirements>
6 6
7 <command> 7 <command>
8 echo "lib1 $reads1 $reads2 $insert $error $orientation" &gt; libraryfile &amp;&amp; 8 echo "lib1 $reads1 $reads2 $insert $error $orientation" &gt; libraryfile &amp;&amp;
9 perl `which SSPACE_Basic_v2.0.pl` -l libraryfile -s $contigs 9 perl `which SSPACE_Basic_v2.0.pl` -l libraryfile -s $contigs
52 <option value="FF">FF</option> 52 <option value="FF">FF</option>
53 <option value="FR" selected="true">FR</option> 53 <option value="FR" selected="true">FR</option>
54 <option value="RF">RF</option> 54 <option value="RF">RF</option>
55 <option value="RR">RR</option> 55 <option value="RR">RR</option>
56 </param> 56 </param>
57 <param name="exten" type="boolean" checked="true" label="Extension (-x)" help="Uncheck for scaffolding only" /> 57 <param name="exten" type="boolean" checked="true" label="Extend the contigs using the paired reads (-x)" help="Uncheck for scaffolding only" />
58 <param name="minoverlap" type="integer" optional="true" min="10" max="50" value="35" label="Extension: minimum number of overlapping bases with the seed/contig during overhang consensus build up (-m)" help="E.g. 32-35 for 36bp reads" /> 58 <param name="minoverlap" type="integer" optional="true" min="10" max="50" value="35" label="Extension: minimum number of overlapping bases with the seed/contig during overhang consensus build up (-m)" help="E.g. 32-35 for 36bp reads" />
59 <param name="numofreads" type="integer" optional="true" value="8" label="Extension: minimum number of reads needed to call an extension (-o)" help="Higher numbers increase reliability of the extension"> 59 <param name="numofreads" type="integer" optional="true" value="8" label="Extension: minimum number of reads needed to call an extension (-o)" help="Higher numbers increase reliability of the extension">
60 <validator type="in_range" min="1" /> 60 <validator type="in_range" min="1" />
61 </param> 61 </param>
62 <param name="max_trim" type="integer" optional="true" value="0" label="Extension: maximum number of bases to trim on the contig end when all possibilities have been exhausted for an extension (-t)"> 62 <param name="max_trim" type="integer" optional="true" value="0" label="Extension: maximum number of bases to trim on the contig end when all possibilities have been exhausted for an extension (-t)">
69 </param> 69 </param>
70 <param name="maxratio" type="float" optional="true" min="0" max="1" value="0.7" label="Scaffolding: maximum link ratio between two best contig pairs (-a)" help="Higher values lead to less accurate scaffolding" /> 70 <param name="maxratio" type="float" optional="true" min="0" max="1" value="0.7" label="Scaffolding: maximum link ratio between two best contig pairs (-a)" help="Higher values lead to less accurate scaffolding" />
71 <param name="contigoverlap" type="integer" optional="true" value="30" label="Scaffolding: minimum overlap required between contigs to merge adjacent contigs in a scaffold (-n)"> 71 <param name="contigoverlap" type="integer" optional="true" value="30" label="Scaffolding: minimum overlap required between contigs to merge adjacent contigs in a scaffold (-n)">
72 <validator type="in_range" min="0" /> 72 <validator type="in_range" min="0" />
73 </param> 73 </param>
74 <param name="mincontig" type="integer" optional="true" value="200" label="Scaffolding: minimum contig size used for scaffold (-z)" help="Filters out contigs below this size"> 74 <param name="mincontig" type="integer" optional="true" value="0" label="Scaffolding: minimum contig length used for scaffold (-z)" help="Filters out contigs below this length. Leave empty or set to 0 for no filtering">
75 <validator type="in_range" min="0" /> 75 <validator type="in_range" min="0" />
76 </param> 76 </param>
77 </inputs> 77 </inputs>
78 78
79 <outputs> 79 <outputs>
90 90
91 SSPACE is a script able to extend and scaffold pre-assembled contigs using one or more mate pairs or paired-end libraries, or even a combination. 91 SSPACE is a script able to extend and scaffold pre-assembled contigs using one or more mate pairs or paired-end libraries, or even a combination.
92 92
93 **License and citation** 93 **License and citation**
94 94
95 This Galaxy tool is Copyright © 2012-2013 `CRS4 Srl.`_ and is released under the `MIT license`_. 95 This Galaxy tool is Copyright © 2012-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
96 96
97 .. _CRS4 Srl.: http://www.crs4.it/ 97 .. _CRS4 Srl.: http://www.crs4.it/
98 .. _MIT license: http://opensource.org/licenses/MIT 98 .. _MIT license: http://opensource.org/licenses/MIT
99 99
100 If you use this tool in Galaxy, please cite |Cuccuru2013|_. 100 You can use this tool only if you agree to the license terms of: `SSPACE basic`_.
101
102 .. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted*
103 .. _Cuccuru2013: http://orione.crs4.it/
104
105 This tool uses `SSPACE basic`_, which is licensed separately. Please cite |Boetzer2011|_.
106 101
107 .. _SSPACE basic: http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/ 102 .. _SSPACE basic: http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/
103
104 If you use this tool, please cite:
105
106 - |Cuccuru2014|_
107 - |Boetzer2011|_.
108
109 .. |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
110 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
108 .. |Boetzer2011| replace:: Boetzer, M., Henkel, C. V., Jansen, H. J., Butler, D., Pirovano, W. (2011) Scaffolding pre-assembled contigs using SSPACE. *Bioinformatics* 27(4), 578-579 111 .. |Boetzer2011| replace:: Boetzer, M., Henkel, C. V., Jansen, H. J., Butler, D., Pirovano, W. (2011) Scaffolding pre-assembled contigs using SSPACE. *Bioinformatics* 27(4), 578-579
109 .. _Boetzer2011: http://bioinformatics.oxfordjournals.org/content/27/4/578 112 .. _Boetzer2011: http://bioinformatics.oxfordjournals.org/content/27/4/578
110 </help> 113 </help>
114 <citations>
115 <citation type="doi">10.1093/bioinformatics/btu135</citation>
116 <citation type="doi">10.1093/bioinformatics/btq683</citation>
117 </citations>
111 </tool> 118 </tool>