Mercurial > repos > peterjc > venn_list

changeset 5:26e35d5133a1 draft

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v0.0.9 - Tool Shed dependency for rpy and limma
author peterjc
date Sat, 10 Oct 2015 08:52:01 -0400
parents 991342eca214
children ea68a1a4c1d9
files tools/venn_list/README.rst tools/venn_list/tool_dependencies.xml tools/venn_list/venn_list.xml
diffstat 3 files changed, 67 insertions(+), 22 deletions(-) [+]
line wrap: on
line diff
--- a/tools/venn_list/README.rst	Wed Apr 29 11:00:41 2015 -0400
+++ b/tools/venn_list/README.rst	Sat Oct 10 08:52:01 2015 -0400
@@ -18,9 +18,8 @@
 ======================
 
 This should be straightforward, Galaxy should automatically download the tool
-and the Biopython dependency.
-
-You will still need to install the R/Bioconductor package limma.
+and the Python dependencies Biopython and rpy, and the R/Bioconductor package
+limma.
 
 
 Manual Installation
@@ -69,6 +68,10 @@
         - Fixed and improved error handling when rpy is not available.
         - Test output relaxed to cope with more variation in PDF output.
         - Declare Biopython dependency via the Tool Shed.
+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).
 ======= ======================================================================
 
 
@@ -81,21 +84,30 @@
 Development has now moved to a dedicated GitHub repository:
 https://github.com/peterjc/pico_galaxy
 
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder::
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+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)::
 
-    $ tar -czf venn_list.tar.gz tools/venn_list/README.rst tools/venn_list/venn_list.* tools/venn_list/tool_dependencies.xml test-data/magic.pdf test-data/venn_list.tabular test-data/rhodopsin_proteins.fasta
+    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/
+    ...
+
+or::
 
-Check this worked::
+    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/
+    ...
+
+To just build and check the tar ball, use::
 
-    $ tar -tzf venn_list.tar.gz
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/venn_list/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
     tools/venn_list/README.rst
+    tools/venn_list/tool_dependencies.xml
     tools/venn_list/venn_list.py
     tools/venn_list/venn_list.xml
-    tools/venn_list/tool_dependencies.xml
     test-data/magic.pdf
+    test-data/rhodopsin_proteins.fasta
     test-data/venn_list.tabular
-    test-data/rhodopsin_proteins.fasta
 
 
 Licence (MIT)
--- a/tools/venn_list/tool_dependencies.xml	Wed Apr 29 11:00:41 2015 -0400
+++ b/tools/venn_list/tool_dependencies.xml	Sat Oct 10 08:52:01 2015 -0400
@@ -1,5 +1,11 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    <package name="limma" version="3.25.3">
+        <repository changeset_revision="b19c06e97bce" name="package_r2_limma_3_25_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="rpy" version="1.0.3">
+        <repository changeset_revision="82170c94ca7c" name="package_rpy_1_0_3" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
     <package name="biopython" version="1.65">
         <repository changeset_revision="dc595937617c" name="package_biopython_1_65" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
--- a/tools/venn_list/venn_list.xml	Wed Apr 29 11:00:41 2015 -0400
+++ b/tools/venn_list/venn_list.xml	Sat Oct 10 08:52:01 2015 -0400
@@ -1,9 +1,11 @@
-<tool id="venn_list" name="Venn Diagram" version="0.0.8">
+<tool id="venn_list" name="Venn Diagram" version="0.0.9">
     <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 -->
@@ -53,22 +55,47 @@
             <param name="set" value="rhodopsin_proteins.fasta"/>
             <param name="lab" value="Rhodopsins"/>
             <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" />
+            <assert_stdout>
+                <has_line line="Doing 1-way Venn Diagram" />
+                <has_line line="Total of 10 IDs" />
+                <has_line line="6 in Rhodopsins" />
+            </assert_stdout>
         </test>
-        <!-- Can't use more than one repeat value in tests (yet)
         <test>
+            <param name="type_select" value="implicit"/>
+            <param name="sets_0|set" value="rhodopsin_proteins.fasta"/>
+            <param name="sets_0|lab" value="Rhodopsins"/>
+            <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"/>
+            <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" />
+            <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="4 in Human" />
+                <has_line line="1 in Human vs Rhodopsin BLAST" />
+            </assert_stdout>
+        </test>
+        <test expect_failure="true" expect_exit_code="1">
             <param name="type_select" value="explicit"/>
             <param name="main" value="venn_list.tabular" ftype="tabular"/>
             <param name="main_lab" value="Some Proteins"/>
-            <param name="count" value="3"/>
-            <param name="set" value="rhodopsin_proteins.fasta"/>
-            <param name="lab" value="Rhodopsins"/>
-            <param name="set" value="four_human_proteins.fasta"/>
-            <param name="lab" value="Human"/>
-            <param name="set" value="blastp_four_human_vs_rhodopsin.tabular"/>
-            <param name="lab" value="Human vs Rhodopsin BLAST"/>
-            <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" />
+            <param name="sets_0|set" value="rhodopsin_proteins.fasta"/>
+            <param name="sets_0|lab" value="Rhodopsins"/>
+            <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"/>
+            <assert_stdout>
+                <has_line line="Doing 3-way Venn Diagram" />
+                <has_line line="Total of 10 IDs" />
+            </assert_stdout>
+            <assert_stderr>
+                <has_text_matching expression="Unexpected ID sp|Q9BS26|ERP44_HUMAN in fasta file *" />
+            </assert_stderr>
         </test>
-        -->
     </tests>
     <help>