Mercurial > repos > peterjc > mira_assembler
changeset 16:f74bc0420db4 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
| author | peterjc |
|---|---|
| date | Wed, 13 May 2015 05:45:01 -0400 |
| parents | fbe9139eb74b |
| children | 557118c7e29e |
| files | tools/mira3/README.rst tools/mira3/mira.py tools/mira3/mira.xml |
| diffstat | 3 files changed, 47 insertions(+), 19 deletions(-) [+] |
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--- a/tools/mira3/README.rst Mon Apr 21 06:57:45 2014 -0400 +++ b/tools/mira3/README.rst Wed May 13 05:45:01 2015 -0400 @@ -30,10 +30,15 @@ * ``mira.xml`` (the Galaxy tool definition) The suggested location is a new ``tools/mira3`` folder. You will also need to -modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool, and also do -this to ``tools_conf.xml.sample`` in order to run any tests:: +modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool by adding +the line:: + + <tool file="mira3/mira.xml" /> - <tool file="mira3/mira.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 -id mira_assembler You will also need to install MIRA, we used version 3.4.1.1. See: @@ -77,6 +82,8 @@ - Correct path issue in automated dependency installation. v0.0.10 - Added a functional test. - Updated URL for automated installation of MIRA v3.4.1.1 +v0.0.11 - Tool definition now embeds citation information. + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). ======= ====================================================================== @@ -89,21 +96,30 @@ Development has now moved to a dedicated GitHub repository: https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_3_4 -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the Galaxy root folder:: +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):: - $ tar -czf mira3_wrapper.tar.gz tools/mira3/README.rst tools/mira3/mira.xml tools/mira3/mira.py tools/mira3/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/empty_file.dat + $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/mira3/ + ... -Check this worked:: +or:: + + $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/mira3/ + ... - $ tar -tzf mira3_wrapper.tar.gz +To just build and check the tar ball, use:: + + $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/mira3/ + ... + $ tar -tzf shed_upload.tar.gz + test-data/empty_file.dat + test-data/tvc_contigs.fasta + test-data/tvc_mini.fastq tools/mira3/README.rst - tools/mira3/mira.xml tools/mira3/mira.py + tools/mira3/mira.xml tools/mira3/tool_dependencies.xml - test-data/tvc_mini.fastq - test-data/tvc_contigs.fasta - test-data/empty_file.dat Licence (MIT)
--- a/tools/mira3/mira.py Mon Apr 21 06:57:45 2014 -0400 +++ b/tools/mira3/mira.py Wed May 13 05:45:01 2015 -0400 @@ -9,7 +9,7 @@ WRAPPER_VER = "0.0.5" #Keep in sync with the XML file -def stop_err(msg, err=1): +def sys_exit(msg, err=1): sys.stderr.write(msg+"\n") sys.exit(err) @@ -33,7 +33,7 @@ mira_ver = get_version() if "V3.4." not in mira_ver: - stop_err("This wrapper is for MIRA V3.4, not %s" % mira_ver) + sys_exit("This wrapper is for MIRA V3.4, not %s" % mira_ver) if "-v" in sys.argv: print "MIRA wrapper version %s," % WRAPPER_VER print mira_ver @@ -44,9 +44,9 @@ n3 = (temp, name, name, name) f = "%s/%s_assembly/%s_d_results" % (temp, name, name) if not os.path.isdir(f): - stop_err("Missing output folder") + sys_exit("Missing output folder") if not os.listdir(f): - stop_err("Empty output folder") + sys_exit("Empty output folder") missing = [] for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta), ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual), @@ -58,7 +58,7 @@ else: shutil.move(old, new) if missing: - stop_err("Missing output files: %s" % ", ".join(missing)) + sys_exit("Missing output files: %s" % ", ".join(missing)) def clean_up(temp, name): folder = "%s/%s_assembly" % (temp, name) @@ -112,7 +112,7 @@ handle.write(cmd + "\n") handle.close() clean_up(temp, name) - stop_err("Return error code %i from command:\n%s" % (return_code, cmd), + sys_exit("Return error code %i from command:\n%s" % (return_code, cmd), return_code) handle.close()
--- a/tools/mira3/mira.xml Mon Apr 21 06:57:45 2014 -0400 +++ b/tools/mira3/mira.xml Wed May 13 05:45:01 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.10"> +<tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.11"> <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description> <requirements> <requirement type="binary">mira</requirement> @@ -189,4 +189,16 @@ Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler </help> + <citations> + <citation type="doi">10.7717/peerj.167</citation> + <citation type="bibtex">@ARTICLE{Chevreux1999-mira3, + author = {B. Chevreux and T. Wetter and S. Suhai}, + year = {1999}, + title = {Genome Sequence Assembly Using Trace Signals and Additional Sequence Information}, + journal = {Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB)} + volume = {99}, + pages = {45-56}, + url = {http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html} + }</citation> + </citations> </tool>