diff tools/fastq_pair_names/README.rst @ 19:20eb53c8a79d draft

planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/fastq_pair_names commit 1700cce8c849ef83cd593bc0ffc547bd4614636a

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+Galaxy tool to extract FASTQ paired read names
+==============================================
+
+This tool is copyright 2014-2015 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 handles FASTQ files with paired
+reads to identify pairs, and can be used to recover missing partners.
+
+The inputs are FASTQ files, and the output is two tabular files. The first
+file has one line per read pair (showing the read pair's name with any
+suffix like ``/1`` or ``/2`` removed). The second file has one line per
+non-paired read (or paired read with unrecognised naming) giving the read
+name.
+
+This tool is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_pair_names
+
+
+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_pair_names.py`` (the Python script)
+* ``fastq_pair_names.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_pair_names``. Then simply add the line::
+
+    <tool file="fastq_pair_names/fastq_pair_names.xml" />
+
+That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial version.
+v0.0.2  - Tool definition now embeds citation information.
+v0.0.3  - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+======= ======================================================================
+
+
+Developers
+==========
+
+Development is on this GitHub repository:
+https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names
+
+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_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/fastq_pair_names/
+    ...
+
+or::
+
+    $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/fastq_pair_names/
+    ...
+
+To just build and check the tar ball, use::
+
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/fastq_pair_names/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    test-data/empty_file.dat
+    test-data/sanger-pairs-mixed.fastq
+    test-data/sanger-pairs-names.tabular
+    tools/fastq_pair_names/README.rst
+    tools/fastq_pair_names/fastq_pair_names.py
+    tools/fastq_pair_names/fastq_pair_names.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.