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phylomatic/phylomatic phylomatic/phylomatic.pl phylomatic/phylomatic.xml phylomatic/phylomatic_README.txt |
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| diff -r de3ada25282e -r 4de3f9572615 phylomatic/phylomatic |
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| Binary file phylomatic/phylomatic has changed |
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| diff -r de3ada25282e -r 4de3f9572615 phylomatic/phylomatic.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phylomatic/phylomatic.pl Thu Jun 21 17:46:55 2012 -0400 |
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| @@ -0,0 +1,10 @@ +#!/usr/bin/perl + +#wrapper written by Roger Ngo and Todd H Oakley, UCSB + +my $file1 = $ARGV[0]; +my $file2 = $ARGV[1]; + +my $run = qx/phylomatic -f $file1 -t $file2 > output.txt 2> errors.txt /; + +print $run; |
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| diff -r de3ada25282e -r 4de3f9572615 phylomatic/phylomatic.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phylomatic/phylomatic.xml Thu Jun 21 17:46:55 2012 -0400 |
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| @@ -0,0 +1,29 @@ +<tool id="phylomatic" name="Phylomatic"> + <description>Run Phylomatic</description> + <command interpreter="perl">./phylomatic.pl $input1 $input2</command> + <inputs> + <param name="input1" type="data" format="txt" label="Phylogenetic Tree" /> + <param name="input2" type="data" format="txt" label="Taxonomy File" /> + </inputs> + + <outputs> + <data from_work_dir="output.txt"/> + </outputs> + + <help> + Phylomatic (Part of Phylocom) + + http://www.phylodiversity.net/phylomatic/phylomatic.html + + The online software takes your list of taxa, and first tries to match them by genus name to the megatree. + Failing that, they are attached by family name. If all the genera appear in the megatree, then that family appears resolved. + If even one genus is missing from the megatree, the returned phylogeny portrays a polytomy of genera. + Currently, species are not included in the megatree, and species within a genus are always returned as polytomies. + (http://www.phylodiversity.net/phylomatic/phylomatic_old.html) + + http://bioinformatics.oxfordjournals.org/content/24/18/2098 + Webb, C. O., Ackerly, D. D. and Kembel, S. W. (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics, 24: 2098-2100. + + </help> +</tool> + |
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| diff -r de3ada25282e -r 4de3f9572615 phylomatic/phylomatic_README.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phylomatic/phylomatic_README.txt Thu Jun 21 17:46:55 2012 -0400 |
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| @@ -0,0 +1,50 @@ +Phylomatic (Part of Phylocom) + + +http://www.phylodiversity.net/phylomatic/phylomatic.html + + + +"The online software takes your list of taxa, and first tries to match them by genus name to the megatree. + +Failing that, they are attached by family name. If all the genera appear in the megatree, then that family appears resolved. + +If even one genus is missing from the megatree, the returned phylogeny portrays a polytomy of genera. + +Currently, species are not included in the megatree, and species within a genus are always returned as polytomies. + (http://www.phylodiversity.net/phylomatic/phylomatic_old.html) +" +http://bioinformatics.oxfordjournals.org/content/24/18/2098 + + +Webb, C. O., Ackerly, D. D. and Kembel, S. W. (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. + Bioinformatics, 24: 2098-2100. + + +Galaxy and Perl wrapper tool implemented by: Roger Ngo and Todd H. Oakley, UCSB + +Included in this package: + +* phylomatic - binary file +* phylomatic.pl - wrapper perl script for Galaxy +* phylomatic.xml - Galaxy tool file +* phylomatic_README.txt - documentation file + +Installation instruction: + +1. Copy the phylomatic binary file to the /bin/ directory of your Galaxy +user account. + +2. Copy phylomatic.pl and phylomatic.xml to a folder in the /galaxy-dist/tools/ +directory. + +3. Add the XML information in tool_conf.xml in /galaxy-dist/ + +4. Restart Galaxy using: + +./run.sh --stop-daemon +./run.sh --reload --daemon + +Known Issues: +Since Galaxy will throw STDERR on warnings generated by programs, the Perl wrappper +script is used to redirect any warnings generated by the binary file to a log file. \ No newline at end of file |