Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
diff phylographics/tab2trees.sh @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
| author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
|---|---|
| date | Tue, 11 Mar 2014 12:19:13 -0700 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phylographics/tab2trees.sh Tue Mar 11 12:19:13 2014 -0700 @@ -0,0 +1,17 @@ +#First call perl script which reads trees and writes +#makeRtrees.pl must be in path! +command -v /var/www/galaxy_dev/galaxy-dist/tools/osiris/phylographics/makeRtrees.pl >/dev/null 2>&1 || { echo > $6 "ERROR: makeRtrees.pl must be available in Galaxy's path. R must be installed with ape and phangorn modules installed."; exit 1; } + + +#$1 infile +#$2 outfile +#$3 tree type (ie phylogram) +#$4 yes|no exclude tips +#$5 yes|no label taxa +#$6 name of Rfile "Rfile" by default in xml +#$7 yes|no to label OTUs with QUERY in title +#$8 yes|no to conduct midpoint rooting + +/var/www/galaxy_dev/galaxy-dist/tools/osiris/phylographics/makeRtrees.pl $1 $2 $3 $4 $5 $7 $8 > $6 2>log.txt + +R --vanilla < $6 2>log.txt