diff tools/plotting/venn_list.xml @ 3:6aae6bc0802d draft

Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub

--- a/tools/plotting/venn_list.xml	Mon May 06 14:05:13 2013 -0400
+++ b/tools/plotting/venn_list.xml	Wed Sep 18 06:19:51 2013 -0400
@@ -1,5 +1,9 @@
-<tool id="venn_list" name="Venn Diagram" version="0.0.3">
+<tool id="venn_list" name="Venn Diagram" version="0.0.6">
   <description>from lists</description>
+  <requirements>
+    <requirement type="python-module">rpy</requirement>
+    <requirement type="python-module">Bio</requirement>
+  </requirements>
   <command interpreter="python">
 venn_list.py
 #if $universe.type_select=="implicit":
@@ -12,6 +16,11 @@
   $s.set $s.set.ext "$s.lab"
 #end for
 $PDF</command>
+  <stdio>
+    <!-- Anything other than zero is an error -->
+    <exit_code range="1:" />
+    <exit_code range=":-1" />
+  </stdio>
   <inputs>
     <param name="main_lab" size="30" type="text" value="Venn Diagram" label="Plot title"/>
     <conditional name="universe">
@@ -32,13 +41,9 @@
   <outputs>
     <data format="pdf" name="PDF" />
   </outputs>
-  <requirements>
-    <requirement type="python-module">rpy</requirement>
-    <requirement type="python-module">Bio</requirement>
-  </requirements>
   <tests>
     <!-- Doesn't seem to work properly, manages to get two sets, both
-         with same FASTA file, but second with default "Group" label.
+         with same FASTA file, but second with default "Group" label. -->
     <test>
       <param name="type_select" value="explicit"/>
       <param name="main" value="venn_list.tabular" ftype="tabular"/>
@@ -47,7 +52,6 @@
       <param name="lab" value="Rhodopsins"/>
       <output name="PDF" file="venn_list1.pdf" ftype="pdf"/>
     </test>
-    -->
     <!-- Can't use more than one repeat value in tests (yet)
     <test>
       <param name="type_select" value="explicit"/>
@@ -101,9 +105,16 @@
 
 The R library is called from Python via rpy, http://rpy.sourceforge.net/
 
-This tool uses Biopython to read SFF files. If you use this tool with
-SFF files in scientific work leading to a publication, please cite the
-Biopython application note:
+If you use this Galaxy tool in work leading to a scientific publication please
+cite:
+
+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
+
+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.