# HG changeset patch
# User peterjc
# Date 1444481325 14400
# Node ID 2a1025bbd6374f371fb9adb7b7dc7af9390dbc9e
# Parent  29d647a7dc3991324880c29f631613e254005416
Tool Shed dependency for rpy and limma

diff -r 29d647a7dc39 -r 2a1025bbd637 tools/venn_list/README.rst
--- a/tools/venn_list/README.rst	Thu May 21 10:51:26 2015 -0400
+++ b/tools/venn_list/README.rst	Sat Oct 10 08:48:45 2015 -0400
@@ -72,6 +72,7 @@
 v0.0.9  - Test with three-way Venn diagram.
         - Includes testing of failure mode.
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+        - Tool Shed dependency for rpy and limma (thanks to Björn Grüning).
 ======= ======================================================================
 
 
@@ -88,12 +89,12 @@
 Planemo commands (which requires you have set your Tool Shed access details in
 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
 
-    $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/
+    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/
     ...
 
 or::
 
-    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/
+    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/
     ...
 
 To just build and check the tar ball, use::
diff -r 29d647a7dc39 -r 2a1025bbd637 tools/venn_list/tool_dependencies.xml
--- a/tools/venn_list/tool_dependencies.xml	Thu May 21 10:51:26 2015 -0400
+++ b/tools/venn_list/tool_dependencies.xml	Sat Oct 10 08:48:45 2015 -0400
@@ -1,5 +1,11 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    <package name="limma" version="3.25.3">
+        <repository changeset_revision="55850b0ff6a3" name="package_r2_limma_3_25_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="rpy" version="1.0.3">
+        <repository changeset_revision="c0eb80864491" name="package_rpy_1_0_3" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
     <package name="biopython" version="1.65">
         <repository changeset_revision="f8d72690eeae" name="package_biopython_1_65" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
diff -r 29d647a7dc39 -r 2a1025bbd637 tools/venn_list/venn_list.xml
--- a/tools/venn_list/venn_list.xml	Thu May 21 10:51:26 2015 -0400
+++ b/tools/venn_list/venn_list.xml	Sat Oct 10 08:48:45 2015 -0400
@@ -2,8 +2,10 @@
     <description>from lists</description>
     <requirements>
         <requirement type="python-module">rpy</requirement>
+        <requirement type="python-module">Bio</requirement>
+        <requirement type="package" version="1.0.3">rpy</requirement>
+        <requirement type="package" version="3.25.3">limma</requirement>
         <requirement type="package" version="1.65">biopython</requirement>
-        <requirement type="python-module">Bio</requirement>
     </requirements>
     <stdio>
         <!-- Anything other than zero is an error -->
@@ -71,7 +73,7 @@
             <assert_stdout>
                 <has_line line="Doing 3-way Venn Diagram" />
                 <has_line line="Inferred total of 10 IDs" />
-		<has_line line="6 in Rhodopsins" />
+                <has_line line="6 in Rhodopsins" />
                 <has_line line="4 in Human" />
                 <has_line line="1 in Human vs Rhodopsin BLAST" />
             </assert_stdout>
@@ -85,7 +87,7 @@
             <param name="sets_1|set" value="four_human_proteins.fasta"/>
             <param name="sets_1|lab" value="Human"/>
             <param name="sets_2|set" value="blastp_four_human_vs_rhodopsin.tabular"/>
-            <param name="sets_2|lab" value="Human vs Rhodopsin BLAST"/>            
+            <param name="sets_2|lab" value="Human vs Rhodopsin BLAST"/>
             <assert_stdout>
                 <has_line line="Doing 3-way Venn Diagram" />
                 <has_line line="Total of 10 IDs" />