diff tools/fastq_paired_unpaired/README.rst @ 4:09f9f0e29e47 draft

v0.0.6 use format_source; v0.0.5 error handling & citation

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+++ b/tools/fastq_paired_unpaired/README.rst	Wed Aug 05 11:06:38 2015 -0400
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+Galaxy tool to divide FASTQ files into paired and unpaired reads
+================================================================
+
+This tool is copyright 2010-2015 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below (MIT licence).
+
+This tool is a short Python script which divides a FASTQ file into paired
+reads, and single or orphan reads. You can have separate files for the
+forward/reverse reads, or have them interleaved in a single file.
+
+Note that the FASTQ variant is unimportant (Sanger, Solexa, Illumina, or even
+Color Space should all work equally well).
+
+This tool is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically download and install
+the tool from the Galaxy Tool Shed, and run the unit tests
+
+
+Manual Installation
+===================
+
+There are just two files to install:
+
+* ``fastq_paired_unpaired.py`` (the Python script)
+* ``fastq_paired_unpaired.xml`` (the Galaxy tool definition)
+
+The suggested location is in the Galaxy folder tools/fastq next to other FASTQ
+tools provided with Galaxy.
+
+You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
+the tool. One suggested location is next to the ``fastq_filter.xml`` entry, or use
+a dedicated folder like ``tools/fastq_paired_unpaired``. Then simply add the line::
+
+    <tool file="fastq_paired_unpaired/fastq_paired_unpaired.xml" />
+
+That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial version, using Biopython
+v0.0.2  - Help text; cope with multiple pairs per template
+v0.0.3  - Galaxy XML wrappers added
+v0.0.4  - Use Galaxy library to handle FASTQ files (avoid Biopython dependency)
+v0.0.5  - Handle Illumina 1.8 style pair names
+v0.0.6  - Record script version when run from Galaxy
+        - Added unit test (FASTQ file using Sanger naming)
+v0.0.7  - Link to Tool Shed added to help text and this documentation.
+v0.0.8  - Use reStructuredText for this README file.
+        - Adopt standard MIT License.
+        - Updated citation information (Cock et al. 2013).
+        - Development moved to GitHub.
+v0.0.9  - Renamed folder and adopted README.rst naming.
+        - Removed some unused code in the Python script.
+v0.1.0  - Switch to using Biopython (easier to use script outside of Galaxy).
+        - Leaves FASTQ plus lines blank (smaller output files).
+        - Tool definition now embeds citation information.
+v0.1.1  - Reorder XML elements (internal change only).
+        - Use ``format_source=...`` tag.
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+======= ======================================================================
+
+
+Developers
+==========
+
+This script and other tools for filtering FASTA, FASTQ and SFF files were
+initially developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
+
+Development has now moved to a dedicated GitHub repository:
+https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired
+
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+Planemo commands (which requires you have set your Tool Shed access details in
+``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
+
+    $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/fastq_paired_unpaired/
+    ...
+
+or::
+
+    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/fastq_paired_unpaired/
+    ...
+
+To just build and check the tar ball, use::
+
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/fastq_paired_unpaired/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    test-data/sanger-pairs-forward.fastq
+    test-data/sanger-pairs-interleaved.fastq
+    test-data/sanger-pairs-mixed.fastq
+    test-data/sanger-pairs-reverse.fastq
+    test-data/sanger-pairs-singles.fastq
+    tools/fastq_paired_unpaired/README.rst
+    tools/fastq_paired_unpaired/fastq_paired_unpaired.py
+    tools/fastq_paired_unpaired/fastq_paired_unpaired.xml
+
+
+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.