diff tools/venn_list/venn_list.xml @ 11:679b6323db03 draft

v0.1.0 now using matplotlib_venn instead of limma R package via rpy. Contribution from Frederic Sapet.

--- a/tools/venn_list/venn_list.xml	Thu May 11 07:02:57 2017 -0400
+++ b/tools/venn_list/venn_list.xml	Wed May 29 04:45:19 2019 -0400
@@ -1,10 +1,10 @@
-<tool id="venn_list" name="Venn Diagram" version="0.0.11">
+<tool id="venn_list" name="Venn Diagram" version="0.1.0">
     <description>from lists</description>
     <requirements>
-        <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>
-        <requirement type="package" version="1.0.3">rpy</requirement>
-        <requirement type="package" version="3.25.3">limma</requirement>
+        <requirement type="package" version="1.1.3">galaxy_sequence_utils</requirement>
         <requirement type="package" version="1.67">biopython</requirement>
+        <requirement type="package" version="2.0.0">matplotlib</requirement>
+        <requirement type="package" version="0.11.5">matplotlib-venn</requirement>
     </requirements>
     <version_command>
 python $__tool_directory__/venn_list.py --version
@@ -126,10 +126,9 @@
 
 **Citations**
 
-The Venn Diagrams are drawn using Gordon Smyth's limma package from
-R/Bioconductor, http://www.bioconductor.org/
+The Venn Diagrams are drawn using Konstantin Tretyakov's matplotlib-venn
+package, https://pypi.org/project/matplotlib-venn/
 
-The R library is called from Python via rpy, http://rpy.sourceforge.net/
 
 If you use this Galaxy tool in work leading to a scientific publication please
 cite:
@@ -137,14 +136,14 @@
 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
 Galaxy tools and workflows for sequence analysis with applications
 in molecular plant pathology. PeerJ 1:e167
-http://dx.doi.org/10.7717/peerj.167
+https://doi.org/10.7717/peerj.167
 
 This tool uses Biopython to read and write SFF files, so you may also wish to
 cite the Biopython application note (and Galaxy too of course):
 
 Cock et al 2009. Biopython: freely available Python tools for computational
 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
-http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
+https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
 
     </help>
     <citations>