| Previous changeset 0:ec6f5279dc01 (2013-10-30) |
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Commit message:
Update Orione citation. Add <citations> tag. Use package_muscle_3_8_31 from iuc. |
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modified:
COPYING muscle.xml tool_dependencies.xml |
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| diff -r ec6f5279dc01 -r 533b3b2a1e66 COPYING --- a/COPYING Wed Oct 30 07:34:04 2013 -0400 +++ b/COPYING Thu Jun 04 11:34:04 2015 -0400 |
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| @@ -1,4 +1,4 @@ -Copyright © 2013 CRS4 Srl. http://www.crs4.it/ +Copyright © 2013-2014 CRS4 Srl. http://www.crs4.it/ Created by: Massimiliano Orsini <massimiliano.orsini@crs4.it> Nicola Soranzo <nicola.soranzo@crs4.it> |
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| diff -r ec6f5279dc01 -r 533b3b2a1e66 muscle.xml --- a/muscle.xml Wed Oct 30 07:34:04 2013 -0400 +++ b/muscle.xml Thu Jun 04 11:34:04 2015 -0400 |
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| @@ -1,7 +1,8 @@ -<tool id="muscle" name="MUSCLE" version="0.0.10"> +<tool id="muscle" name="MUSCLE" version="0.0.11"> <description>multiple aligner</description> <requirements> <requirement type="package" version="3.8.31">muscle</requirement> + <requirement type="set_environment">FASTA_MAX_SIZE</requirement> </requirements> <version_command>muscle -version</version_command> <command> @@ -24,6 +25,8 @@ <data name="output" format="fasta" label="${tool.name} on ${on_string}: aligned sequences"/> <data name="log" format="txt" label="${tool.name} on ${on_string}: log"/> </outputs> + <tests> + </tests> <help> **What it does** @@ -31,20 +34,26 @@ **License and citation** -This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_. +This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_. .. _CRS4 Srl.: http://www.crs4.it/ .. _MIT license: http://opensource.org/licenses/MIT -If you use this tool in Galaxy, please cite |Cuccuru2013|_. - -.. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted* -.. _Cuccuru2013: http://orione.crs4.it/ - -This tool uses `MUSCLE`_, which is licensed separately. Please cite |Edgar2004|_. +You can use this tool only if you agree to the license terms of: `MUSCLE`_. .. _MUSCLE: http://drive5.com/muscle/ + +If you use this tool, please cite: + +- |Cuccuru2014|_ +- |Edgar2004|_. + +.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929 +.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928 .. |Edgar2004| replace:: Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. *Nucleic Acids Res.* 32(5), 1792-1797 .. _Edgar2004: http://nar.oxfordjournals.org/content/32/5/1792 </help> + <citations> + <citation type="doi">10.1093/nar/gkh340</citation> + </citations> </tool> |
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| diff -r ec6f5279dc01 -r 533b3b2a1e66 tool_dependencies.xml --- a/tool_dependencies.xml Wed Oct 30 07:34:04 2013 -0400 +++ b/tool_dependencies.xml Thu Jun 04 11:34:04 2015 -0400 |
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| @@ -1,27 +1,11 @@ <?xml version="1.0"?> <tool_dependency> + <set_environment version="1.0"> + <!-- MUSCLE may require a lot of memory and computation time for a medium/large input multi-FASTA file, therefore a limit on the file size is enforced by the tool. +Change the FASTA_MAX_SIZE variable in the installed env.sh file to adjust this limit to your needs and available resources. --> + <environment_variable action="set_to" name="FASTA_MAX_SIZE">100000</environment_variable> + </set_environment> <package name="muscle" version="3.8.31"> - <install version="1.0"> - <actions> - <action type="download_by_url" target_filename="muscle3.8.31.tar.gz">http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz</action> - <!-- When compiling, need to remove the '-static' linker option from the src/mk file used by src/Makefile --> - <action type="shell_command">sed -i 's/-static//g' src/mk</action> - <action type="shell_command">make -C src/</action> - <action type="move_file"> - <source>src/muscle</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - <action type="set_environment"> - <environment_variable name="FASTA_MAX_SIZE" action="set_to">100000</environment_variable> - </action> - </actions> - </install> - <readme> -MUSCLE may require a lot of memory and computation time for a medium/large input multi-FASTA file, therefore a limit on the file size is enforced by the tool. -Change the FASTA_MAX_SIZE variable in the installed env.sh file to adjust this limit to your needs and available resources. - </readme> + <repository changeset_revision="8f20b47725d8" name="package_muscle_3_8_31" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |