diff tools/filters/seq_select_by_id.rst @ 3:19e26966ed3e draft

Uploaded v0.0.6, handles Biopython dependency via the ToolShed, adopted MIT license, using reStructuredTest for the README file. No functional changes.

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+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.