diff sspace.xml @ 2:bc4451edb703 draft

Update Orione citation. Update dependency to SSPACE Basic v2.1 . Add <citations>.

--- a/sspace.xml	Fri Feb 21 04:17:55 2014 -0500
+++ b/sspace.xml	Mon Oct 27 14:11:57 2014 -0400
@@ -1,7 +1,7 @@
-<tool id="sspace" name="SSPACE" version="1.0.6">
+<tool id="sspace" name="SSPACE" version="1.0.7">
   <description>scaffolder</description>
   <requirements>
-    <requirement type="package" version="2.0">sspace</requirement>
+    <requirement type="package" version="2.1">sspace</requirement>
   </requirements>
 
   <command>
@@ -54,7 +54,7 @@
       <option value="RF">RF</option>
       <option value="RR">RR</option>
     </param>
-    <param name="exten" type="boolean" checked="true" label="Extension (-x)" help="Uncheck for scaffolding only" />
+    <param name="exten" type="boolean" checked="true" label="Extend the contigs using the paired reads (-x)" help="Uncheck for scaffolding only" />
     <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" />
     <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">
       <validator type="in_range" min="1" />
@@ -71,7 +71,7 @@
     <param name="contigoverlap" type="integer" optional="true" value="30" label="Scaffolding: minimum overlap required between contigs to merge adjacent contigs in a scaffold (-n)">
       <validator type="in_range" min="0" />
     </param>
-    <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">
+    <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">
       <validator type="in_range" min="0" />
     </param>
   </inputs>
@@ -92,20 +92,27 @@
 
 **License and citation**
 
-This Galaxy tool is Copyright © 2012-2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
+This Galaxy tool is Copyright © 2012-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
 
 .. _CRS4 Srl.: http://www.crs4.it/
 .. _MIT license: http://opensource.org/licenses/MIT
 
-If you use this tool in Galaxy, please cite |Cuccuru2013|_.
-
-.. |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*
-.. _Cuccuru2013: http://orione.crs4.it/
-
-This tool uses `SSPACE basic`_, which is licensed separately. Please cite |Boetzer2011|_.
+You can use this tool only if you agree to the license terms of: `SSPACE basic`_.
 
 .. _SSPACE basic: http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/
+
+If you use this tool, please cite:
+
+- |Cuccuru2014|_
+- |Boetzer2011|_.
+
+.. |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
+.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
 .. |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
 .. _Boetzer2011: http://bioinformatics.oxfordjournals.org/content/27/4/578
   </help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btu135</citation>
+    <citation type="doi">10.1093/bioinformatics/btq683</citation>
+  </citations>
 </tool>