changeset 70:bd26a18387ae draft

Uploaded

--- a/phylogenomics_analysis.xml	Thu Mar 02 10:08:10 2017 -0500
+++ b/phylogenomics_analysis.xml	Thu Mar 16 14:31:52 2017 -0400
@@ -1,5 +1,5 @@
-<tool id="plant_tribes_phylogenomics_analysis" name="Create multiple sequence alignments" version="0.6.0">
-    <description>and inferred maximum likelihood phylogenies</description>
+<tool id="plant_tribes_phylogenomics_analysis" name="PhylogenomicsAnalysis" version="0.6.0">
+    <description>builds gene family multiple sequence alignments and their corresponding phylogenies</description>
     <requirements>
         <requirement type="package" version="0.6">plant_tribes_phylogenomics_analysis</requirement>
     </requirements>
@@ -297,42 +297,39 @@
     </help>
     <citations>
         <citation type="bibtex">
-            @unpublished{None,
-            author = {Eric Wafula},
-            title = {None},
+            @misc{None,
+            journal = {None},
+            author = {1. Wafula EK},
+            title = {Manuscript in preparation},
             year = {None},
-            url = {https://github.com/dePamphilis/PlantTribes}
-            }
+            url = {https://github.com/dePamphilis/PlantTribes},}
         </citation>
-        <citation type="doi">10.1093/bioinformatics/btw412</citation>
         <citation type="bibtex">
-            @published{Research in Computational Molecular Biology (RECOMB) (pp. 177–191),
-            author = {Mirarab, S., Nguyen, N., Warnow, T.},
-            title = {PASTA: Ultra-Large Multiple Sequence Alignment. In R. Sharan
-            (Ed.)},
+            @article{Mirarab2014,
+            journal = {Research in Computational Molecular Biology (RECOMB)},
+            author = {2. Mirarab S, Nguyen N, Warnow T},
+            title = {PASTA: Ultra-Large Multiple Sequence Alignment. In R. Sharan (Ed.)},
             year = {2014},
-            url = {https://github.com/smirarab/pasta}
-            }
+            pages = {177–191},
+            url = {https://github.com/smirarab/pasta},}
         </citation>
         <citation type="bibtex">
-            @published{Bioinformatics,
-            author = {Salvador Capella-Gutierrez, Jose M. Silla-Martinez, Toni
-            Gabaldon},
-            title = {trimAl: a tool for automated alignment trimming in large-scale
-            phylogenetic analyses},
+            @article{Salvador2009,
+            journal = {Bioinformatics},
+            author = {3. Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T},
+            title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses},
             year = {2009},
-            url = {http://trimal.cgenomics.org}
-            }
+            url = {http://trimal.cgenomics.org},}
         </citation>
         <citation type="bibtex">
-            @published{Bioinformatics,
-            author = {A. Stamatakis},
-            title = {RAxML Version 8: A tool for Phylogenetic Analysis and
-            Post-Analysis of Large Phylogenies},
+            @article{Stamatakis2014,
+            journal = {Bioinformatics},
+            author = {4. Stamatakis A},
+            title = {RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies},
             year = {2014},
-            url = {http://sco.h-its.org/exelixis/web/software/raxml/index.html}
-            }
+            url = {http://sco.h-its.org/exelixis/web/software/raxml/index.html},}
         </citation>
         <citation type="doi">10.1371/journal.pone.0009490</citation>
+        <citation type="doi">10.1093/bioinformatics/btw412</citation>
     </citations>
 </tool>