Mercurial > repos > peterjc > venn_list
changeset 4:29fcd027d67a draft
Uploaded v0.0.6 take 1, simple test (which currently fails)
| author | peterjc |
|---|---|
| date | Thu, 16 May 2013 12:43:57 -0400 |
| parents | bacb7dfa846c |
| children | 51fe47a5a803 |
| files | test-data/venn_list.tabular test-data/venn_list1.pdf tools/plotting/venn_list.py tools/plotting/venn_list.txt tools/plotting/venn_list.xml |
| diffstat | 5 files changed, 520 insertions(+), 12 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/venn_list.tabular Thu May 16 12:43:57 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|
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--- a/tools/plotting/venn_list.py Thu May 16 12:43:20 2013 -0400 +++ b/tools/plotting/venn_list.py Thu May 16 12:43:57 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(">"):
--- a/tools/plotting/venn_list.txt Thu May 16 12:43:20 2013 -0400 +++ b/tools/plotting/venn_list.txt Thu May 16 12:43:57 2013 -0400 @@ -32,6 +32,9 @@ ======= 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. Developers @@ -40,10 +43,10 @@ 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 +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.* +tar -czf venn_list.tar.gz tools/plotting/venn_list.* test-data/venn_list1.pdf test-data/venn_list.tabular Check this worked: @@ -51,6 +54,8 @@ tools/plotting/venn_list.py tools/plotting/venn_list.txt tools/plotting/venn_list.xml +test-data/venn_list1.pdf +test-data/venn_list.tabular Licence (MIT/BSD style)
--- a/tools/plotting/venn_list.xml Thu May 16 12:43:20 2013 -0400 +++ b/tools/plotting/venn_list.xml Thu May 16 12:43:57 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"/>