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Repository coverage_stats
Owner: peterjc
Synopsis: BAM coverage statistics using samtools idxstats and depth
This tool runs the commands ``samtools idxstats`` and ``samtools depth`` from
the SAMtools toolkit, and parses their output to produce a consise summary of
the coverage information for each reference sequence.
Type: unrestricted
Revision: 2:7254ece0c0ff
This revision can be installed: True
Times cloned / installed: 441

Repository README files - may contain important installation or license information

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:: 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 ```` (internal change only). - Single quote command line arguments (internal change only). ======= ====================================================================== 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.

Contents of this repository

Name Description Version Minimum Galaxy Version
using samtools idxstats and depth 0.0.5 any

Categories
Assembly - Tools for working with assemblies
SAM - Tools for manipulating alignments in the SAM format