Mercurial > repos > peterjc > seq_select_by_id

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/filters/repository_dependencies.xml	Mon Jul 29 09:13:13 2013 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<repositories description="This requires Biopython as a dependency.">
+<!-- Leave out the tool shed and revision to get the current
+     tool shed and latest revision at the time of upload -->
+<repository changeset_revision="5d0c54f7fea2" name="package_biopython_1_61" owner="biopython" toolshed="http://toolshed.g2.bx.psu.edu" />
+</repositories>
--- a/tools/filters/seq_select_by_id.py	Mon Apr 15 12:28:51 2013 -0400
+++ b/tools/filters/seq_select_by_id.py	Mon Jul 29 09:13:13 2013 -0400
@@ -17,10 +17,10 @@
 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.

 This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute UK.
-All rights reserved. See accompanying text file for licence details (MIT/BSD
-style).
+All rights reserved. See accompanying text file for licence details (MIT
+license).

-This is version 0.0.4 of the script.
+This is version 0.0.6 of the script.
 """
 import sys

@@ -29,7 +29,7 @@
     sys.exit(err)

 if "-v" in sys.argv or "--version" in sys.argv:
-    print "v0.0.4"
+    print "v0.0.6"
     sys.exit(0)

 #Parse Command Line
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/filters/seq_select_by_id.rst	Mon Jul 29 09:13:13 2013 -0400
@@ -0,0 +1,118 @@
+Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID
+===============================================================
+
+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 extract
+sequences from a FASTA, QUAL, FASTQ, or SFF file based on the list of IDs given
+by a column of a tabular file. The output order follows that of the tabular file,
+and if there are duplicates in the tabular file, there will be duplicates in the
+output sequence file.
+
+This tool is available from the Galaxy Tool Shed at:
+
+* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
+
+See also the sister tools to filter sequence files according to IDs from column(s)
+of a tabular file (where the output order follows the sequence file, and any
+duplicate IDs are ignored) and rename sequences:
+
+* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
+* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename
+
+
+Automated Installation
+======================
+
+This should be straightforward using the Galaxy Tool Shed, which should be
+able to automatically install the dependency on Biopython, and then install
+this tool and run its unit tests.
+
+
+Manual Installation
+===================
+
+There are just two files to install to use this tool from within Galaxy:
+
+* seq_select_by_id.py (the Python script)
+* seq_select_by_id.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/seq_select_by_id.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_select_by_id
+
+You will also need to install Biopython 1.54 or later. That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1   - Initial version.
+v0.0.3   - Ignore blank lines in input.
+v0.0.4   - Record script version when run from Galaxy.
+         - Basic unit test included.
+v0.0.5   - Check for errors using Python script's return code.
+v0.0.6   - Link to Tool Shed added to help text and this documentation.
+         - Automatic installation of Biopython dependency.
+         - Use reStructuredText for this README file.
+         - Adopt standard MIT License.
+======= ======================================================================
+
+
+Developers
+==========
+
+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://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+    $ tar -czf seq_select_by_id.tar.gz tools/filters/seq_select_by_id.* tools/filters/repository_dependencies.xml test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular
+
+Check this worked::
+
+    $ tar -tzf seq_select_by_id.tar.gz
+    tools/filters/seq_select_by_id.py
+    tools/filters/seq_select_by_id.rst
+    tools/filter/seq_select_by_id.xml
+    tools/filters/repository_dependencies.xml
+    test-data/k12_ten_proteins.fasta
+    test-data/k12_hypothetical.fasta
+    test-data/k12_hypothetical.tabular
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
--- a/tools/filters/seq_select_by_id.txt	Mon Apr 15 12:28:51 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID
-===============================================================
-
-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 extract
-sequences from a FASTA, QUAL, FASTQ, or SFF file based on the list of IDs given
-by a column of a tabular file. The output order follows that of the tabular file,
-and if there are duplicates in the tabular file, there will be duplicates in the
-output sequence file.
-
-See also the sister tool to filter sequence files according to IDs from column(s)
-of a tabular file, where the output order follows the sequence file, and any
-duplicate IDs are ignored.
-
-There are just two files to install:
-
-* seq_select_by_id.py (the Python script)
-* seq_select_by_id.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/seq_select_by_id.xml" />
-
-You will also need to install Biopython 1.54 or later. That's it.
-
-
-History
-=======
-
-v0.0.1 - Initial version.
-v0.0.3 - Ignore blank lines in input.
-v0.0.4 - Record script version when run from Galaxy.
-       - Basic unit test included.
-
-
-Developers
-==========
-
-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://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder:
-
-$ tar -czf seq_select_by_id.tar.gz tools/filters/seq_select_by_id.* test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular
-
-Check this worked:
-
-$ tar -tzf seq_select_by_id.tar.gz
-filter/seq_select_by_id.py
-filter/seq_select_by_id.txt
-filter/seq_select_by_id.xml
-test-data/k12_ten_proteins.fasta
-test-data/k12_hypothetical.fasta
-test-data/k12_hypothetical.tabular
-
-
-Licence (MIT/BSD style)
-=======================
-
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
-
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
--- a/tools/filters/seq_select_by_id.xml	Mon Apr 15 12:28:51 2013 -0400
+++ b/tools/filters/seq_select_by_id.xml	Mon Jul 29 09:13:13 2013 -0400
@@ -1,9 +1,14 @@
-<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.4">
+<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.6">
 	<description>from a tabular file</description>
 	<version_command interpreter="python">seq_select_by_id.py --version</version_command>
 	<command interpreter="python">
 seq_select_by_id.py $input_tabular $column $input_file $input_file.ext $output_file
 	</command>
+        <stdio>
+                <!-- Anything other than zero is an error -->
+                <exit_code range="1:" />
+                <exit_code range=":-1" />
+        </stdio>
 	<inputs>
 		<param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file to select from" help="FASTA, QUAL, FASTQ, or SFF format." />
 		<param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/>
@@ -54,5 +59,7 @@
 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_select_by_id
 	</help>
 </tool>