diff tools/filters/get_orfs_or_cdss.txt @ 1:922d69bd5258 draft

Uploaded v0.0.2, fixes labelling issue on reverse strand.

--- a/tools/filters/get_orfs_or_cdss.txt	Thu Jan 19 10:17:10 2012 -0500
+++ b/tools/filters/get_orfs_or_cdss.txt	Tue Jan 29 10:19:01 2013 -0500
@@ -1,7 +1,7 @@
 Galaxy tool to find ORFs or simple CDSs
 =======================================
 
-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.
 
@@ -15,9 +15,9 @@
 * get_orfs_or_cdss.py (the Python script)
 * get_orfs_or_cdss.xml (the Galaxy tool definition)
 
-The suggested location is in the Galaxy folder tools/filters next to the tool
+If you are installing this manually (rather than via the Tool Shed), the
+suggested location is in the Galaxy folder tools/filters next to the tool
 for calling sff_extract.py for converting SFF to FASTQ or FASTA + QUAL.
-
 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
 tool. One suggested location is in the filters section. Simply add the line:
 
@@ -25,13 +25,19 @@
 
 You will also need to install Biopython 1.54 or later. If you want to run
 the unit tests, include this line in tools_conf.xml.sample and the sample
-FASTA files under the test-data directory. That's it.
+FASTA files under the test-data directory. Then:
+
+./run_functional_tests.sh -id get_orfs_or_cdss
+
+That's it.
 
 
 History
 =======
 
 v0.0.1 - Initial version.
+v0.0.2 - Correct labelling issue on reverse strand.
+       - Use the new <stdio> settings in the XML wrappers to catch errors
 
 
 Developers
@@ -43,7 +49,7 @@
 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
 the following command from the Galaxy root folder:
 
-tar -czf get_orfs_or_cdss.tar.gz tools/filters/get_orfs_or_cdss.*
+tar -czf get_orfs_or_cdss.tar.gz tools/filters/get_orfs_or_cdss.* test-data/get_orf_input*.fasta
 
 Check this worked:
 
@@ -51,6 +57,14 @@
 filter/get_orfs_or_cdss.py
 filter/get_orfs_or_cdss.txt
 filter/get_orfs_or_cdss.xml
+test-data/get_orf_input.Suis_ORF.nuc.fasta
+test-data/get_orf_input.Suis_ORF.prot.fasta
+test-data/get_orf_input.t11_nuc_out.fasta
+test-data/get_orf_input.t11_open_nuc_out.fasta
+test-data/get_orf_input.t11_open_prot_out.fasta
+test-data/get_orf_input.t11_prot_out.fasta
+test-data/get_orf_input.t1_nuc_out.fasta
+test-data/get_orf_input.t1_prot_out.fasta
 
 
 Licence (MIT/BSD style)