diff tools/fastq/fastq_paired_unpaired.rst @ 3:6a14074bc810 draft

Uploaded v0.0.8, automated Biopython dependency handling via ToolShed; MIT license; reST markup for README file.

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+Galaxy tool to divide FASTQ files into paired and unpaired reads
+================================================================
+
+This tool is copyright 2010-2013 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 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. Simply
+add the line::
+
+    <tool file="fastq/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.
+======= ======================================================================
+
+
+Developers
+==========
+
+This script and other tools for filtering FASTA, FASTQ and SFF files are
+currently being developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+    $ tar -czf fastq_paired_unpaired.tar.gz tools/fastq/fastq_paired_unpaired.* test-data/sanger-pairs-*.fastq
+
+Check this worked::
+
+    $ tar -tzf fastq_paired_unpaired.tar.gz
+    tools/fastq/fastq_paired_unpaired.py
+    tools/fastq/fastq_paired_unpaired.rst
+    tools/fastq/fastq_paired_unpaired.xml
+    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
+
+
+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.