Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate phylographics/tab2trees.sh @ 0:5b9a38ec4a39 draft default tip

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