| Next changeset 1:533b3b2a1e66 (2015-06-04) |
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COPYING muscle.xml tool_dependencies.xml |
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| diff -r 000000000000 -r ec6f5279dc01 COPYING --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Wed Oct 30 07:34:04 2013 -0400 |
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| @@ -0,0 +1,23 @@ +Copyright © 2013 CRS4 Srl. http://www.crs4.it/ +Created by: +Massimiliano Orsini <massimiliano.orsini@crs4.it> +Nicola Soranzo <nicola.soranzo@crs4.it> + +Permission is hereby granted, free of charge, to any person obtaining a +copy of this software and associated documentation files (the +"Software"), to deal in the Software without restriction, including +without limitation the rights to use, copy, modify, merge, publish, +distribute, sublicense, and/or sell copies of the Software, and to +permit persons to whom the Software is furnished to do so, subject to +the following conditions: + +The above copyright notice and this permission notice shall be included +in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF +MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. +IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY +CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, +TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE +SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
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| diff -r 000000000000 -r ec6f5279dc01 muscle.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/muscle.xml Wed Oct 30 07:34:04 2013 -0400 |
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| @@ -0,0 +1,50 @@ +<tool id="muscle" name="MUSCLE" version="0.0.10"> + <description>multiple aligner</description> + <requirements> + <requirement type="package" version="3.8.31">muscle</requirement> + </requirements> + <version_command>muscle -version</version_command> + <command> + FASTA_MAX_SIZE=\${FASTA_MAX_SIZE:-100000}; + if [ `stat -c "%s" $multifasta` -gt \$FASTA_MAX_SIZE ]; then echo "Multi-FASTA file is bigger than the configured limit for MUSCLE (\$FASTA_MAX_SIZE bytes)." >&2; exit 1; fi; + muscle -quiet -in $multifasta -out $output -log $log + #if str($maxiters) + -maxiters $maxiters + #end if + #if $diags + -diags + #end if + </command> + <inputs> + <param name="multifasta" type="data" format="fasta" label="Multi-FASTA file" /> + <param name="maxiters" type="integer" value="2" min="1" max="16" optional="true" label="Maximum number of iterations to run (-maxiters)" help="Set to 2 for large datasets where refinement (iterations 3+) is too slow." /> + <param name="diags" type="boolean" label="Diagonal optimization (-diags)" help="Speed up the algorithm, especially for closely related sequences, at the expense of some reduction in accuracy" /> + </inputs> + <outputs> + <data name="output" format="fasta" label="${tool.name} on ${on_string}: aligned sequences"/> + <data name="log" format="txt" label="${tool.name} on ${on_string}: log"/> + </outputs> + <help> +**What it does** + +This tool performs multiple sequence alignment using MUSCLE. + +**License and citation** + +This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_. + +.. _CRS4 Srl.: http://www.crs4.it/ +.. _MIT license: http://opensource.org/licenses/MIT + +If you use this tool in Galaxy, please cite |Cuccuru2013|_. + +.. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted* +.. _Cuccuru2013: http://orione.crs4.it/ + +This tool uses `MUSCLE`_, which is licensed separately. Please cite |Edgar2004|_. + +.. _MUSCLE: http://drive5.com/muscle/ +.. |Edgar2004| replace:: Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. *Nucleic Acids Res.* 32(5), 1792-1797 +.. _Edgar2004: http://nar.oxfordjournals.org/content/32/5/1792 + </help> +</tool> |
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| diff -r 000000000000 -r ec6f5279dc01 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Oct 30 07:34:04 2013 -0400 |
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| @@ -0,0 +1,27 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="muscle" version="3.8.31"> + <install version="1.0"> + <actions> + <action type="download_by_url" target_filename="muscle3.8.31.tar.gz">http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz</action> + <!-- When compiling, need to remove the '-static' linker option from the src/mk file used by src/Makefile --> + <action type="shell_command">sed -i 's/-static//g' src/mk</action> + <action type="shell_command">make -C src/</action> + <action type="move_file"> + <source>src/muscle</source> + <destination>$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> + </package> +</tool_dependency> |