Mercurial > repos > peterjc > samtools_idxstats
changeset 4:242f1a5a9277 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats commit ddda833946bc691eacf9c116695bda3a1bbdbf19
| author | peterjc |
|---|---|
| date | Wed, 13 May 2015 10:34:12 -0400 |
| parents | 3070949d8fd7 |
| children | 08834fedb0d0 |
| files | tools/samtools_idxstats/README.rst tools/samtools_idxstats/samtools_idxstats.py tools/samtools_idxstats/samtools_idxstats.xml tools/samtools_idxstats/tool_dependencies.xml |
| diffstat | 4 files changed, 35 insertions(+), 23 deletions(-) [+] |
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--- a/tools/samtools_idxstats/README.rst Fri Nov 21 07:02:43 2014 -0500 +++ b/tools/samtools_idxstats/README.rst Wed May 13 10:34:12 2015 -0400 @@ -1,7 +1,7 @@ Galaxy wrapper for samtools idxstats ==================================== -This wrapper is copyright 2013-2014 by Peter Cock, The James Hutton Institute +This wrapper is copyright 2013-2015 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. @@ -52,6 +52,8 @@ v0.0.1 - Initial public release v0.0.2 - Use quoted filenames when calling samtools (in case of spaces etc) v0.0.3 - Embed samtools citation in tool XML. +v0.0.4 - Reorder XML elements (internal change only). + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). ======= ====================================================================== @@ -61,20 +63,30 @@ Development is on this GitHub repository: https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the Galaxy root folder:: - $ tar -czf samtools_idxstats.tar.gz tools/samtools_idxstats/README.rst tools/samtools_idxstats/samtools_idxstats.xml tools/samtools_idxstats/samtools_idxstats.py tools/samtools_idxstats/tool_dependencies.xml test-data/ex1.bam test-data/ex1.idxstats.tabular +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/samtools_idxstats/ + ... -Check this worked:: +or:: + + $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_idxstats/ + ... - $ tar -tzf samtools_idxstats.tar.gz - tools/samtools_idxstats/README.rst - tools/samtools_idxstats/samtools_idxstats.xml - tools/samtools_idxstats/samtools_idxstats.py - tools/samtools_idxstats/tool_dependencies.xml +To just build and check the tar ball, use:: + + $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/samtools_idxstats/ + ... + $ tar -tzf shed_upload.tar.gz test-data/ex1.bam test-data/ex1.idxstats.tabular + tools/samtools_idxstats/README.rst + tools/samtools_idxstats/samtools_idxstats.py + tools/samtools_idxstats/samtools_idxstats.xml + tools/samtools_idxstats/tool_dependencies.xml Licence (MIT)
--- a/tools/samtools_idxstats/samtools_idxstats.py Fri Nov 21 07:02:43 2014 -0500 +++ b/tools/samtools_idxstats/samtools_idxstats.py Wed May 13 10:34:12 2015 -0400 @@ -21,22 +21,22 @@ cmd = "samtools 2>&1 | grep -i ^Version" sys.exit(os.system(cmd)) -def stop_err(msg, error_level=1): +def sys_exit(msg, error_level=1): """Print error message to stdout and quit with given error level.""" sys.stderr.write("%s\n" % msg) sys.exit(error_level) if len(sys.argv) != 4: - stop_err("Require three arguments: BAM, BAI, tabular filenames") + sys_exit("Require three arguments: BAM, BAI, tabular filenames") bam_filename, bai_filename, tabular_filename = sys.argv[1:] if not os.path.isfile(bam_filename): - stop_err("Input BAM file not found: %s" % bam_filename) + sys_exit("Input BAM file not found: %s" % bam_filename) if not os.path.isfile(bai_filename): if bai_filename == "None": - stop_err("Error: Galaxy did not index your BAM file") - stop_err("Input BAI file not found: %s" % bai_filename) + sys_exit("Error: Galaxy did not index your BAM file") + sys_exit("Input BAI file not found: %s" % bai_filename) #Assign sensible names with real extensions, and setup symlinks: tmp_dir = tempfile.mkdtemp() @@ -58,4 +58,4 @@ os.rmdir(tmp_dir) if return_code: - stop_err("Return code %i from command:\n%s" % (return_code, cmd)) + sys_exit("Return code %i from command:\n%s" % (return_code, cmd))
--- a/tools/samtools_idxstats/samtools_idxstats.xml Fri Nov 21 07:02:43 2014 -0500 +++ b/tools/samtools_idxstats/samtools_idxstats.xml Wed May 13 10:34:12 2015 -0400 @@ -1,9 +1,14 @@ -<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.3"> +<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.4"> <description>samtools idxstats</description> <requirements> <requirement type="binary">samtools</requirement> <requirement type="package" version="0.1.19">samtools</requirement> </requirements> + <stdio> + <!-- Assume anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> <version_command interpreter="python">samtools_idxstats.py --version</version_command> <command interpreter="python">samtools_idxstats.py "$input_bam" "${input_bam.metadata.bam_index}" "$out_tabular"</command> <inputs> @@ -12,11 +17,6 @@ <outputs> <data name="out_tabular" format="tabular" label="$input_bam.name (idxstats)" /> </outputs> - <stdio> - <!-- Assume anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> <tests> <test> <param name="input_bam" value="ex1.bam" ftype="bam" />
--- a/tools/samtools_idxstats/tool_dependencies.xml Fri Nov 21 07:02:43 2014 -0500 +++ b/tools/samtools_idxstats/tool_dependencies.xml Wed May 13 10:34:12 2015 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="samtools" version="0.1.19"> - <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>