Mercurial > repos > peterjc > mummer
changeset 1:a8efa5191c47 draft
Uploaded v0.0.2, corrects typo in tool ID, included citation markup in XML.
| author | peterjc |
|---|---|
| date | Tue, 28 Oct 2014 06:39:30 -0400 |
| parents | 8acf86c61f8e |
| children | 63470b69cc1d |
| files | tools/mummer/README.rst tools/mummer/mummer.xml tools/mummer/tool_dependencies.xml |
| diffstat | 3 files changed, 15 insertions(+), 9 deletions(-) [+] |
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--- a/tools/mummer/README.rst Fri May 23 07:20:04 2014 -0400 +++ b/tools/mummer/README.rst Tue Oct 28 06:39:30 2014 -0400 @@ -5,7 +5,7 @@ (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. -This is a wrapper for the command suite MUMmer v3. +This is a dotplot tool wrapping functionality from the MUMmer v3 suite. S. Kurtz et al. (2004). Versatile and open software for comparing large genomes. @@ -21,7 +21,8 @@ This should be straightforward, Galaxy should automatically download and install the MUMmer files. -It also needs gnuplot, and ps2pdf. +It also needs the tools ``gnuplot`` and ``ps2pdf`` to be installed and on the +system ``$PATH``. Manual Installation @@ -46,7 +47,7 @@ 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:: - $ ./run_functional_tests.sh -id mummer_wrapper + $ ./run_tests.sh -id mummerplot_wrapper That's it. @@ -57,7 +58,9 @@ ======= ====================================================================== Version Changes ------- ---------------------------------------------------------------------- -v0.0.1 - Initial public release +v0.0.1 - Initial public release. +v0.0.2 - Correct typo in Tool identifier. + - Include MUMmer citation in Galaxy XML markup. ======= ======================================================================
--- a/tools/mummer/mummer.xml Fri May 23 07:20:04 2014 -0400 +++ b/tools/mummer/mummer.xml Tue Oct 28 06:39:30 2014 -0400 @@ -1,5 +1,5 @@ -<tool id="mumer_wrapper" name="MUMmer" version="0.0.1"> - <description>Draw dotplot with mummer/nucmer/promer/mummerplot</description> +<tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.2"> + <description>Combine mummer/nucmer/promer with mummerplot</description> <requirements> <requirement type="binary">ps2pdf</requirement> <requirement type="binary">nucmer</requirement> @@ -43,8 +43,8 @@ <help> **What it does** -Takes two FASTA files (*species A* and *species B*), compairs them using one -of the MUMmer 3 tools (``mummer``, ``nucmer``, or ``promer``), comparing both +Takes two FASTA files (*species A* and *species B*), compares them using one +of the MUMmer 3 tools (``mummer``, ``nucmer``, or ``promer``), checking both strands, and then draws a dotplot using ``mummerplot``. The full MUMmer suite is more flexible and capable than this limited wrapper. @@ -65,4 +65,7 @@ This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mummer </help> + <citations> + <citation type="doi">10.1186/gb-2004-5-2-r12</citation> + </citations> </tool>
--- a/tools/mummer/tool_dependencies.xml Fri May 23 07:20:04 2014 -0400 +++ b/tools/mummer/tool_dependencies.xml Tue Oct 28 06:39:30 2014 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="mummer" version="3.23"> - <repository changeset_revision="020178be49ee" name="package_mummer_3_23" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="020178be49ee" name="package_mummer_3_23" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>