Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
comparison 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 |
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| -1:000000000000 | 0:5b9a38ec4a39 |
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| 1 #First call perl script which reads trees and writes | |
| 2 #makeRtrees.pl must be in path! | |
| 3 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; } | |
| 4 | |
| 5 | |
| 6 #$1 infile | |
| 7 #$2 outfile | |
| 8 #$3 tree type (ie phylogram) | |
| 9 #$4 yes|no exclude tips | |
| 10 #$5 yes|no label taxa | |
| 11 #$6 name of Rfile "Rfile" by default in xml | |
| 12 #$7 yes|no to label OTUs with QUERY in title | |
| 13 #$8 yes|no to conduct midpoint rooting | |
| 14 | |
| 15 /var/www/galaxy_dev/galaxy-dist/tools/osiris/phylographics/makeRtrees.pl $1 $2 $3 $4 $5 $7 $8 > $6 2>log.txt | |
| 16 | |
| 17 R --vanilla < $6 2>log.txt |