# HG changeset patch # User peterjc # Date 1368722637 14400 # Node ID 29fcd027d67a0c6d930922d21898cf8961c0d820 # Parent bacb7dfa846c5ede6787ff9a2fb17cb7ca8716fd Uploaded v0.0.6 take 1, simple test (which currently fails) diff -r bacb7dfa846c -r 29fcd027d67a test-data/venn_list.tabular --- /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| diff -r bacb7dfa846c -r 29fcd027d67a test-data/venn_list1.pdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/venn_list1.pdf Thu May 16 12:43:57 2013 -0400 @@ -0,0 +1,488 @@ +%PDF-1.4 +%ρ\r +1 0 obj +<< +/CreationDate (D:20110419150236) +/ModDate (D:20110419150236) +/Title (R 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bacb7dfa846c -r 29fcd027d67a tools/plotting/venn_list.py --- 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(">"): diff -r bacb7dfa846c -r 29fcd027d67a tools/plotting/venn_list.txt --- 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) diff -r bacb7dfa846c -r 29fcd027d67a tools/plotting/venn_list.xml --- 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 @@ - + from lists + + rpy + Bio + venn_list.py #if $universe.type_select=="implicit": @@ -12,6 +16,11 @@ $s.set $s.set.ext "$s.lab" #end for $PDF + + + + + @@ -32,13 +41,9 @@ - - rpy - Bio - @@ -47,7 +52,6 @@ - -->