Mercurial > repos > peterjc > samtools_idxstats
changeset 3:3070949d8fd7 draft
Uploaded v0.0.3, embedded citation
| author | peterjc |
|---|---|
| date | Fri, 21 Nov 2014 07:02:43 -0500 |
| parents | 93b8db68dde4 |
| children | 242f1a5a9277 |
| 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, 17 insertions(+), 12 deletions(-) [+] |
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--- a/tools/samtools_idxstats/README.rst Wed Nov 13 07:05:15 2013 -0500 +++ b/tools/samtools_idxstats/README.rst Fri Nov 21 07:02:43 2014 -0500 @@ -1,7 +1,7 @@ Galaxy wrapper for samtools idxstats ==================================== -This wrapper is copyright 2013 by Peter Cock, The James Hutton Institute +This wrapper is copyright 2013-2014 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. @@ -26,19 +26,19 @@ To install the wrapper copy or move the following files under the Galaxy tools folder, e.g. in a ``tools/samtools_idxstats`` folder: -* samtools_idxstats.xml (the Galaxy tool definition) -* samtools_idxstats.py (the Python wrapper script) -* README.rst (this file) +* ``samtools_idxstats.xml`` (the Galaxy tool definition) +* ``samtools_idxstats.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="samtools_idxstats/samtools_idxstats.xml" /> -If you wish to run the unit tests, also add this to tools_conf.xml.sample -and move/copy the test-data files under Galaxy's test-data folder. Then:: +If you wish to run the unit tests, also move/copy the ``test-data/`` files +under Galaxy's ``test-data/`` folder. Then:: - $ ./run_functional_tests.sh -id samtools_idxstats + $ ./run_tests.sh -id samtools_idxstats That's it. @@ -50,13 +50,15 @@ Version Changes ------- ---------------------------------------------------------------------- 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. ======= ====================================================================== Developers ========== -Development is one this GitHub repository: +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
--- a/tools/samtools_idxstats/samtools_idxstats.py Wed Nov 13 07:05:15 2013 -0500 +++ b/tools/samtools_idxstats/samtools_idxstats.py Fri Nov 21 07:02:43 2014 -0500 @@ -17,7 +17,7 @@ if "-v" in sys.argv or "--version" in sys.argv: #Galaxy seems to invert the order of the two lines - print "(Galaxy wrapper v0.0.1)" + print "(Galaxy wrapper v0.0.2)" cmd = "samtools 2>&1 | grep -i ^Version" sys.exit(os.system(cmd)) @@ -49,7 +49,7 @@ assert os.path.isfile(bam_file + ".bai"), bam_file #Run samtools idxstats: -cmd = "samtools idxstats %s > %s" % (bam_file, tabular_filename) +cmd = 'samtools idxstats "%s" > "%s"' % (bam_file, tabular_filename) return_code = os.system(cmd) #Remove the temp symlinks:
--- a/tools/samtools_idxstats/samtools_idxstats.xml Wed Nov 13 07:05:15 2013 -0500 +++ b/tools/samtools_idxstats/samtools_idxstats.xml Fri Nov 21 07:02:43 2014 -0500 @@ -1,4 +1,4 @@ -<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.1"> +<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.3"> <description>samtools idxstats</description> <requirements> <requirement type="binary">samtools</requirement> @@ -73,4 +73,7 @@ This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + </citations> </tool>
--- a/tools/samtools_idxstats/tool_dependencies.xml Wed Nov 13 07:05:15 2013 -0500 +++ b/tools/samtools_idxstats/tool_dependencies.xml Fri Nov 21 07:02:43 2014 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="samtools" version="0.1.19"> - <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>