Mercurial > repos > greg > gene_family_phylogeny_builder

comparison gene_family_phylogeny_builder.xml @ 47:22d6092baa99 draft

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author greg
date Fri, 08 Sep 2017 10:27:00 -0400
parents 8262754dc5f9
children 0c9847a598fc
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46:8262754dc5f9 47:22d6092baa99
14 #set rooting_order = $rooting_order_file_cond.rooting_order 14 #set rooting_order = $rooting_order_file_cond.rooting_order
15 #end if 15 #end if
16 #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates 16 #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates
17 #end if 17 #end if
18 mkdir $input_dir && 18 mkdir $input_dir &&
19 #for $dce in $input: 19 #for $i in $input:
20 #set filename = $dce.element_object.filename 20 #set filename = $i.filename
21 ln -s $filename $input_dir 21 ln -s $filename $input_dir
22 #end for 22 #end for
23 GeneFamilyPhylogenyBuilder 23 GeneFamilyPhylogenyBuilder
24 --orthogroup_aln '$input_dir' 24 --orthogroup_aln '$input_dir'
25 --scaffold '$scaffold.fields.path' 25 --scaffold '$scaffold.fields.path'