Mercurial > repos > peterjc > samtools_depad
changeset 2:8e1e3a1ecad7 draft
Uploaded v0.0.2, embeds citation
| author | peterjc |
|---|---|
| date | Fri, 28 Nov 2014 11:47:41 -0500 |
| parents | 8c1a4a771903 |
| children | a908d8f33a17 |
| files | tools/samtools_depad/README.rst tools/samtools_depad/samtools_depad.xml tools/samtools_depad/tool_dependencies.xml |
| diffstat | 3 files changed, 11 insertions(+), 7 deletions(-) [+] |
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--- a/tools/samtools_depad/README.rst Tue Apr 15 12:00:11 2014 -0400 +++ b/tools/samtools_depad/README.rst Fri Nov 28 11:47:41 2014 -0500 @@ -21,7 +21,7 @@ Manual Installation =================== -This expects samtools to be on the $PATH, and was tested using v0.1.19. +This expects samtools to be on the ``$PATH``, and was tested using v0.1.19. To install the wrapper copy or move the following files under the Galaxy tools folder, e.g. in a ``tools/samtools_depad`` folder: @@ -35,10 +35,10 @@ <tool file="samtools_depad/samtools_depad.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_depad + $ ./run_tests.sh -id samtools_depad That's it. @@ -49,7 +49,8 @@ ======= ====================================================================== Version Changes ------- ---------------------------------------------------------------------- -v0.0.1 - Initial public release +v0.0.1 - Initial public release. +v0.0.2 - Embed samtools citation in the tool XML. ======= ======================================================================
--- a/tools/samtools_depad/samtools_depad.xml Tue Apr 15 12:00:11 2014 -0400 +++ b/tools/samtools_depad/samtools_depad.xml Fri Nov 28 11:47:41 2014 -0500 @@ -1,4 +1,4 @@ -<tool id="samtools_depad" name="Depad SAM/BAM file" version="0.0.1"> +<tool id="samtools_depad" name="Depad SAM/BAM file" version="0.0.2"> <description>samtools depad</description> <requirements> <requirement type="binary">samtools</requirement> @@ -56,4 +56,7 @@ 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_depad </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + </citations> </tool>
--- a/tools/samtools_depad/tool_dependencies.xml Tue Apr 15 12:00:11 2014 -0400 +++ b/tools/samtools_depad/tool_dependencies.xml Fri Nov 28 11:47:41 2014 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="samtools" version="0.1.19"> - <repository changeset_revision="36aa94676939" 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>