# HG changeset patch
# User crs4
# Date 1414433517 14400
# Node ID bc4451edb703ac125447e2f8e172c972bedbb913
# Parent  93fa7ecb5292f34fdf8d90bbf840a56471a939d4
Update Orione citation. Update dependency to SSPACE Basic v2.1 . Add <citations>.

diff -r 93fa7ecb5292 -r bc4451edb703 readme.rst
--- a/readme.rst	Fri Feb 21 04:17:55 2014 -0500
+++ b/readme.rst	Mon Oct 27 14:11:57 2014 -0400
@@ -14,11 +14,12 @@
 
 (where N is the number of CPU cores allocated by the job runner for this tool) to the file
 
-  <tool_dependencies_dir>/sspace/2.0/crs4/sspace/<hash_string>/env.sh
+  <tool_dependencies_dir>/sspace/2.1/crs4/sspace/<hash_string>/env.sh
 
 Version history
 ---------------
 
+- Release 2: Update Orione citation. Update dependency to SSPACE Basic v2.1 . Add <citations>.
 - Release 1: Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
 - Release 0: Initial release in the Tool Shed.
 
diff -r 93fa7ecb5292 -r bc4451edb703 sspace.xml
--- 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>
diff -r 93fa7ecb5292 -r bc4451edb703 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Feb 21 04:17:55 2014 -0500
+++ b/tool_dependencies.xml	Mon Oct 27 14:11:57 2014 -0400
@@ -1,17 +1,18 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="sspace" version="2.0">
+  <package name="bowtie" version="1.0.0">
+    <repository changeset_revision="9fcaaedbbfd6" name="package_bowtie_1_0_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="sspace" version="2.1">
     <install version="1.0">
       <actions>
-        <action type="download_by_url" target_filename="SSPACE-BASIC-2.0_linux-x86_64.zip">http://www.baseclear.com/download.php?file_id=1038</action>
-        <!-- fix for Perl >= 5.16.0-->
-        <action type="shell_command">sed -i -e 's/require "getopts.pl"/use Getopt::Std/' -e 's/&amp;Getopts/getopts/' SSPACE_Basic_v2.0.pl</action>
+        <action target_filename="sspace_basic-2.1.tar.gz" type="download_by_url">https://github.com/nsoranzo/sspace_basic/archive/v2.1.tar.gz</action>
         <action type="move_directory_files">
           <source_directory>.</source_directory>
           <destination_directory>$INSTALL_DIR</destination_directory>
         </action>
         <action type="set_environment">
-          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
         </action>
       </actions>
     </install>