| Previous changeset 3:b2e648e55ed7 (2013-09-18) Next changeset 5:e8f15b0136cd (2017-02-01) |
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Commit message:
v0.0.10 internal changes; v0.0.9 citation |
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modified:
tools/nlstradamus/README.rst tools/nlstradamus/nlstradamus.xml tools/nlstradamus/tool_dependencies.xml |
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| diff -r b2e648e55ed7 -r 1458e60f3fd0 tools/nlstradamus/README.rst --- a/tools/nlstradamus/README.rst Wed Sep 18 06:15:33 2013 -0400 +++ b/tools/nlstradamus/README.rst Wed Aug 05 12:23:05 2015 -0400 |
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| @@ -1,7 +1,7 @@ Galaxy wrapper for NLStradamus v1.7 or v1.8 (C++ version) ========================================================= -This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute +This wrapper is copyright 2011-2015 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below (MIT licence). @@ -35,25 +35,24 @@ Manual Installation =================== -This wrapper expects the compiled C++ binary "NLStradamus" to be on the system -PATH. +This wrapper expects the compiled C++ binary "NLStradamus" to be on the ``$PATH``. To install the wrapper copy or move the following files under the Galaxy tools folder, e.g. in a tools/protein_analysis folder: -* nlstradamus.xml (the Galaxy tool definition) -* nlstradamus.txt (this README file) +* ``nlstradamus.xml`` (the Galaxy tool definition) +* ``nlstradamus.txt`` (this README file) -You will also need to modify the tools_conf.xml file to tell Galaxy to offer the -tool. If you are using other protein analysis tools like TMHMM or SignalP, put -it next to them. Just add the line (matching the chosen install path):: +You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer +the tool. If you are using other protein analysis tools like TMHMM or SignalP, +put it next to them. Just add the line (matching the chosen install path):: <tool file="protein_analysis/nlstradamus.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 nlstradamus + $ ./run_tests.sh -id nlstradamus That's it. @@ -77,33 +76,47 @@ - Adopted standard MIT licence. - Updated citation information (Cock et al. 2013). - Development moved to GitHub, https://github.com/peterjc/pico_galaxy +v0.0.9 - Tool definition now embeds citation information. +v0.0.10 - Reorder XML elements (internal change only). + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). ======= ====================================================================== Developers ========== -This script and related tools are being developed on the following hg branch: +This script and related tools were initially developed on the following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools Development has now moved to a dedicated GitHub repository: https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus -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):: + + $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/nlstradamus/ + ... + +or:: - $ tar -czf nlstradmus.tar.gz tools/nlstradamus/README.rst tools/nlstradamus/nlstradamus.xml tools/nlstradamus/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.nlstradamus.tabular test-data/empty.fasta test-data/empty_nlstradamus.tabular + $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/nlstradamus/ + ... + +To just build and check the tar ball, use:: -Check this worked:: - - $ tar -tzf nlstradmus.tar.gz + $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/nlstradamus/ + ... + $ tar -tzf shed_upload.tar.gz + test-data/empty.fasta + test-data/empty_nlstradamus.tabular + test-data/four_human_proteins.fasta + test-data/four_human_proteins.nlstradamus.tabular tools/nlstradamus/README.rst tools/nlstradamus/nlstradamus.xml tools/nlstradamus/tool_dependencies.xml test-data/four_human_proteins.fasta - test-data/four_human_proteins.nlstradamus.tabular - test-data/empty.fasta - test-data/empty_nlstradamus.tabular Licence (MIT) |
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| diff -r b2e648e55ed7 -r 1458e60f3fd0 tools/nlstradamus/nlstradamus.xml --- a/tools/nlstradamus/nlstradamus.xml Wed Sep 18 06:15:33 2013 -0400 +++ b/tools/nlstradamus/nlstradamus.xml Wed Aug 05 12:23:05 2015 -0400 |
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| @@ -1,13 +1,17 @@ -<tool id="nlstradamus" name="NLStradamus" version="0.0.8"> +<tool id="nlstradamus" name="NLStradamus" version="0.0.10"> <description>Find nuclear localization signals (NLSs) in protein sequences</description> - <command> - NLStradamus -i $fasta_file -t $threshold -m $model -a $algorithm -tab > $tabular_file - </command> + <requirements> + <requirement type="binary">NLStradamus</requirement> + <requirement type="package" version="1.8">NLStradamus</requirement> + </requirements> <stdio> <!-- Assume anything other than zero is an error --> <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> + <command> + NLStradamus -i $fasta_file -t $threshold -m $model -a $algorithm -tab > $tabular_file + </command> <inputs> <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> <param name="model" type="select" display="radio" label="Model"> @@ -26,16 +30,12 @@ <outputs> <data name="tabular_file" format="tabular" label="NLStradamus results" /> </outputs> - <requirements> - <requirement type="binary">NLStradamus</requirement> - <requirement type="package" version="1.8">NLStradamus</requirement> - </requirements> <tests> <test> <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" /> <param name="model" value="1" /> <param name="algorithm" value="1" /> - <param name="threshold" value="0.6" /> + <param name="threshold" value="0.6" /> <output name="tabular_file" file="four_human_proteins.nlstradamus.tabular" ftype="tabular" /> </test> <test> @@ -90,4 +90,8 @@ This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus </help> + <citations> + <citation type="doi">10.7717/peerj.167</citation> + <citation type="doi">10.1186/1471-2105-10-202</citation> + </citations> </tool> |
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| diff -r b2e648e55ed7 -r 1458e60f3fd0 tools/nlstradamus/tool_dependencies.xml --- a/tools/nlstradamus/tool_dependencies.xml Wed Sep 18 06:15:33 2013 -0400 +++ b/tools/nlstradamus/tool_dependencies.xml Wed Aug 05 12:23:05 2015 -0400 |
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| @@ -4,7 +4,7 @@ <install version="1.0"> <actions> <action type="download_by_url">http://www.moseslab.csb.utoronto.ca/NLStradamus/NLStradamus/NLStradamus.1.8.tar.gz</action> - <!-- Although v1.7 used a subfolder in the tar-ball, v1.8 did not --> + <!-- Although v1.7 used a subfolder in the tar-ball, v1.8 did not --> <action type="shell_command">g++ NLStradamus.cpp -o NLStradamus -O3</action> <action type="move_file"><source>NLStradamus</source><destination>$INSTALL_DIR/</destination></action> <action type="set_environment"> |