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changeset 3:6aae6bc0802d draft

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Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
author peterjc
date Wed, 18 Sep 2013 06:19:51 -0400
parents c96bef0643dc
children 991342eca214
files test-data/rhodopsin_proteins.fasta test-data/venn_list.tabular test-data/venn_list1.pdf tools/plotting/venn_list.py tools/plotting/venn_list.rst tools/plotting/venn_list.txt tools/plotting/venn_list.xml
diffstat 7 files changed, 175 insertions(+), 88 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rhodopsin_proteins.fasta	Wed Sep 18 06:19:51 2013 -0400
@@ -0,0 +1,43 @@
+>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]
+MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT
+PLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVC
+KPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVV
+HFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQG
+SNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA
+
+>gi|3024260|sp|P56514.1|OPSD_BUFBU RecName: Full=Rhodopsin
+MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRT
+PLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVC
+KPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVV
+HFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQG
+SEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTEASSVSSSQ
+VSPA
+
+>gi|283855846|gb|ADB45242.1| rhodopsin [Cynopterus brachyotis]
+VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLA
+VADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGE
+NHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIF
+FCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTL
+PAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS
+
+>gi|283855823|gb|ADB45229.1| rhodopsin [Myotis pilosus]
+VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLA
+VANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGE
+NHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIF
+FCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTI
+PAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS
+
+>gi|223523|prf||0811197A rhodopsin [Bos taurus]
+MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRT
+PLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVC
+KPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYTPHEETNNESFVIYMFVVH
+FIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGS
+DFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA
+
+>gi|12583665|dbj|BAB21486.1| fresh water form rod opsin [Conger myriaster]
+MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRT
+PLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVC
+KPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTC
+HFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQG
+STFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTEASSVSSSS
+VSPA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/venn_list.tabular	Wed Sep 18 06:19:51 2013 -0400
@@ -0,0 +1,10 @@
+gi|57163783|ref|NP_001009242.1|
+gi|3024260|sp|P56514.1|OPSD_BUFBU
+gi|283855846|gb|ADB45242.1|
+gi|283855823|gb|ADB45229.1|
+gi|223523|prf||0811197A
+gi|12583665|dbj|BAB21486.1|
+gi|155008482|gb|ABS89278.1|
+gi|4887221|gb|AAD32241.1|
+gi|4506527|ref|NP_000530.1|
+gi|20465209|gb|AAM11432.1|
Binary file test-data/venn_list1.pdf has changed
--- a/tools/plotting/venn_list.py	Mon May 06 14:05:13 2013 -0400
+++ b/tools/plotting/venn_list.py	Wed Sep 18 06:19:51 2013 -0400
@@ -5,7 +5,7 @@
 (formerly SCRI), UK. All rights reserved.
 See accompanying text file for licence details (MIT/BSD style).
 
-This is version 0.0.3 of the script.
+This is version 0.0.4 of the script.
 """
 
 
@@ -46,8 +46,9 @@
 def load_ids(filename, filetype):
     if filetype=="tabular":
         for line in open(filename):
-            if not line.startswith("#"):
-                yield line.rstrip("\n").split("\t",1)[0]
+            line = line.rstrip("\n")
+            if line and not line.startswith("#"):
+                yield line.split("\t",1)[0]
     elif filetype=="fasta":
         for line in open(filename):
             if line.startswith(">"):
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/plotting/venn_list.rst	Wed Sep 18 06:19:51 2013 -0400
@@ -0,0 +1,97 @@
+Galaxy tool to draw a Venn Diagram with up to 3 sets
+====================================================
+
+This tool is copyright 2011 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below.
+
+This tool is a short Python script (using both the Galaxy and Biopython library
+functions) to extract ID lists from tabular, FASTA, FASTQ or SFF files to build
+sets, which are then drawn using the R limma package function vennDiagram
+(called from Python using rpy).
+
+There are just two files to install:
+
+* venn_list.py (the Python script)
+* venn_list.xml (the Galaxy tool definition)
+
+The suggested location is in the Galaxy folder tools/plotting next to other
+graph drawing tools.
+
+You will also need to install Biopython 1.54 or later, and the R/Bioconductor
+pacakge limma. You should already have rpy installed for other Galaxy tools.
+
+You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
+tool. The suggested location is in the "Graph/Display Data" section. Simply add
+the line::
+
+  <tool file="plotting/venn_list.xml" />
+
+If you wish to run the unit tests, also add this to tools_conf.xml.sample and
+move/copy the test-data files under Galaxy's test-data folder. Then::
+
+    ./run_functional_tests.sh -id venn_list
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.3  - Initial public release.
+v0.0.4  - Ignore blank lines when loading IDs from tabular files
+v0.0.5  - Explicit Galaxy error handling of return codes
+v0.0.6  - Added unit tests.
+        - Use reStructuredText for this README file.
+        - Adopt standard MIT licence.
+        - Updated citation information (Cock et al. 2013).
+        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
+======= ======================================================================
+
+
+Developers
+==========
+
+This script and related tools are being developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+Development has now moved to a dedicated GitHub repository:
+https://github.com/peterjc/pico_galaxy/tree/master/tools
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+    $ tar -czf venn_list.tar.gz tools/plotting/venn_list.* test-data/venn_list1.pdf test-data/venn_list.tabular test-data/rhodopsin_proteins.fasta
+
+Check this worked::
+
+    $ tar -tzf venn_list.tar.gz
+    tools/plotting/venn_list.py
+    tools/plotting/venn_list.rst
+    tools/plotting/venn_list.xml
+    test-data/venn_list1.pdf
+    test-data/venn_list.tabular
+    test-data/rhodopsin_proteins.fasta
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
--- a/tools/plotting/venn_list.txt	Mon May 06 14:05:13 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,75 +0,0 @@
-Galaxy tool to draw a Venn Diagram with up to 3 sets
-====================================================
-
-This tool is copyright 2011 by Peter Cock, The James Hutton Institute
-(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-See the licence text below.
-
-This tool is a short Python script (using both the Galaxy and Biopython library
-functions) to extract ID lists from tabular, FASTA, FASTQ or SFF files to build
-sets, which are then drawn using the R limma package function vennDiagram
-(called from Python using rpy).
-
-There are just two files to install:
-
-* venn_list.py (the Python script)
-* venn_list.xml (the Galaxy tool definition)
-
-The suggested location is in the Galaxy folder tools/plotting next to other
-graph drawing tools.
-
-You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
-tool. The suggested location is in the "Graph/Display Data" section. Simply add
-the line:
-
-<tool file="plotting/venn_list.xml" />
-
-You will also need to install Biopython 1.54 or later, and the R/Bioconductor
-pacakge limma. You should already have rpy installed for other Galaxy tools.
-
-
-History
-=======
-
-v0.0.3 - Initial public release.
-
-
-Developers
-==========
-
-This script and related tools are being developed on the following hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/tools
-
-For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder:
-
-tar -czf venn_list.tar.gz tools/plotting/venn_list.*
-
-Check this worked:
-
-$ tar -tzf venn_list.tar.gz
-tools/plotting/venn_list.py
-tools/plotting/venn_list.txt
-tools/plotting/venn_list.xml
-
-
-Licence (MIT/BSD style)
-=======================
-
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
-
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
--- 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.