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

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

0:9cff9a1176ea

Galaxy tool to find ORFs or simple CDSs
=======================================

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 Biopython library functions)
to search nucleotide sequences for open reading frames (ORFs) or coding

There are just two files to install:

* 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
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:

<tool file="filters/get_orfs_or_cdss.xml" />

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.


History
=======

v0.0.1 - Initial version.


Developers
==========

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 get_orfs_or_cdss.tar.gz tools/filters/get_orfs_or_cdss.*

Check this worked:

$ tar -tzf get_orfs_or_cdss.tar.gz
filter/get_orfs_or_cdss.py
filter/get_orfs_or_cdss.txt
filter/get_orfs_or_cdss.xml


Licence (MIT/BSD style)
=======================

1:922d69bd5258

Galaxy tool to find ORFs or simple CDSs
=======================================

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.

This tool is a short Python script (using Biopython library functions)
to search nucleotide sequences for open reading frames (ORFs) or coding

There are just two files to install:

* get_orfs_or_cdss.py (the Python script)
* get_orfs_or_cdss.xml (the Galaxy tool definition)

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:

<tool file="filters/get_orfs_or_cdss.xml" />

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. 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
==========

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 get_orfs_or_cdss.tar.gz tools/filters/get_orfs_or_cdss.* test-data/get_orf_input*.fasta

Check this worked:

$ tar -tzf get_orfs_or_cdss.tar.gz
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)
=======================