| Previous changeset 1:6ce8634e2035 (2013-04-22) Next changeset 3:16a1a5ae98e9 (2013-05-08) |
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Commit message:
Uploaded v0.0.3, add links to Tool Shed in documentation. Unit test passes locally. |
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modified:
tools/filters/seq_rename.txt tools/filters/seq_rename.xml |
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| diff -r 6ce8634e2035 -r b51633a69a92 tools/filters/seq_rename.txt --- a/tools/filters/seq_rename.txt Mon Apr 22 13:48:03 2013 -0400 +++ b/tools/filters/seq_rename.txt Tue May 07 09:52:31 2013 -0400 |
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| @@ -1,7 +1,7 @@ Galaxy tool to renamed FASTA, QUAL, FASTQ or SFF sequences ========================================================== -This tool is copyright 2011 by Peter Cock, The James Hutton Institute +This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. @@ -11,8 +11,20 @@ and if there are duplicates in the input sequence file, there will be duplicates in the output sequence file. +This tool is available from the Galaxy Tool Shed, +http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename + See also the sister tools to filter or select sequence files according to IDs -from column(s) of tabular file. +from column(s) of tabular file: +http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id +http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id + + +Automated Installation +====================== + +This should be straightforward, provided you have installed Biopython 1.54 or later. +Galaxy should automatically install the Python script, and run the unit tests. Manual Installation @@ -31,6 +43,11 @@ <tool file="filters/seq_rename.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 seq_rename + You will also need to install Biopython 1.54 or later. That's it. @@ -41,6 +58,7 @@ v0.0.2 - Record script version when run from Galaxy. - Add unit test. - Check for errors using Python script's return code. +v0.0.3 - Link to Tool Shed added to help text and this documentation. Developers |
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| diff -r 6ce8634e2035 -r b51633a69a92 tools/filters/seq_rename.xml --- a/tools/filters/seq_rename.xml Mon Apr 22 13:48:03 2013 -0400 +++ b/tools/filters/seq_rename.xml Tue May 07 09:52:31 2013 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="seq_rename" name="Rename sequences" version="0.0.2"> +<tool id="seq_rename" name="Rename sequences" version="0.0.3"> <description>with ID mapping from a tabular file</description> <version_commmand interpreter="python">seq_rename.py --version</version_commmand> <command interpreter="python"> @@ -64,5 +64,7 @@ molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. +This tool is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename </help> </tool> |