Mercurial > repos > greg > phylogenomics_analysis

comparison phylogenomics_analysis.xml @ 9:0ca4bba49038 draft

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author greg
date Thu, 05 Jan 2017 14:38:49 -0500
parents 9c43870f6c51
children b3712c598290
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8:9c43870f6c51 9:0ca4bba49038
11 <regex match="Exception:" /> 11 <regex match="Exception:" />
12 </stdio> 12 </stdio>
13 <command> 13 <command>
14 <![CDATA[ 14 <![CDATA[
15 #import os 15 #import os
16 #import sys
17 #if not os.exists($orthogroup_faa.extra_files_path):
18 print > sys.stderr("The select input is not a valid list of sequences classified into gene family clusters, select another input.")
19 #end if
16 #set src_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta') 20 #set src_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta')
17 #set dest_dir = $output.extra_files_path 21 #set dest_dir = $output.extra_files_path
18 mkdir -p $dest_dir && 22 mkdir -p $dest_dir &&
19 PhylogenomicsAnalysis 23 PhylogenomicsAnalysis
20 --orthogroup_faa "$orthogroup_faa.extra_files_path" 24 --orthogroup_faa "$orthogroup_faa.extra_files_path"