diff tools/coverage_stats/README.rst @ 4:ed501717f6cd draft default tip

"Update all the pico_galaxy tools on main Tool Shed"

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+++ b/tools/coverage_stats/README.rst	Fri Apr 16 22:34:30 2021 +0000
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+BAM coverage statistics using samtools idxstats and depth
+=========================================================
+
+This tool is copyright 2014-2017 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below.
+
+Internally this tool uses the command-line samtools suite.
+
+This tool is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/coverage_stats
+
+
+Automated Installation
+======================
+
+This should be straightforward, provided your Galaxy is setup to use Conda and
+BioConda for dependencies - Galaxy should then automatically download and
+install the expected version of samtools.
+
+
+Manual Installation
+===================
+
+This expects samtools to be on the ``$PATH``, and was tested using v1.3.1.
+
+To install the wrapper copy or move the following files under the Galaxy tools
+folder, e.g. in a ``tools/coverage_stats`` folder:
+
+* ``coverage_stats.xml`` (the Galaxy tool definition)
+* ``coverage_stats.py`` (the Python wrapper script)
+* ``README.rst`` (this file)
+
+You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
+the tool. Just add the line, perhaps under the NGS tools section::
+
+  <tool file="coverage_stats/coverage_stats.xml" />
+
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
+
+    $ ./run_tests.sh -id coverage_stats
+
+That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial public release
+v0.0.2  - Cope with samtools' default depth limit using modified samtools,
+          see https://github.com/samtools/samtools/pull/322
+v0.0.3  - Cope with no coverage in final contigs.
+v0.0.4  - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+v0.0.5  - Expose new ``samtools depth -d ...`` argument added in samtools v1.3
+        - Depends on samtools v1.4.1 via Conda, which IS NOT AVAILABLE as a
+          legacy Tool Shed package.
+        - Apply the new maximum depth parameter within the script to ensure
+          excess coverage is clear by getting the max coverage equal to the
+          max depth setting (the raw output from samtools is more fuzzy).
+        - Report total length and overall mean coverage in stdout.
+        - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only).
+v0.0.6  - Python 3 compatibility fix.
+v0.1.0  - Provide proper command line API for the Python script.
+======= ======================================================================
+
+
+Developers
+==========
+
+Development is on this GitHub repository:
+https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats
+
+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 -t testtoolshed --check_diff tools/coverage_stats/
+    ...
+
+or::
+
+    $ planemo shed_update -t toolshed --check_diff tools/coverage_stats/
+    ...
+
+To just build and check the tar ball, use::
+
+    $ planemo shed_upload --tar_only tools/coverage_stats/
+    ...
+    $ tar -tzf shed_upload.tar.gz
+    tools/coverage_stats/README.rst
+    tools/coverage_stats/coverage_stats.xml
+    tools/coverage_stats/coverage_stats.py
+    ...
+
+
+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.
+
+NOTE: This is the licence for the Galaxy Wrapper only.
+samtools is available and licenced separately.