Mercurial > repos > greg > phylogenomics_analysis

comparison phylogenomics_analysis.xml @ 13:b37db5a8ed13 draft

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Uploaded
author greg
date Thu, 05 Jan 2017 15:15:47 -0500
parents 16861f56079f
children a8a4f6009451
comparison
equal deleted inserted replaced
12:16861f56079f 13:b37db5a8ed13
20 $sys.exit(1) 20 $sys.exit(1)
21 #end if 21 #end if
22 #set src_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta') 22 #set src_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta')
23 #set num_orthogroup_faa = 0 23 #set num_orthogroup_faa = 0
24 #for f in $os.listdir($src_dir): 24 #for f in $os.listdir($src_dir):
25 #if $f.endswith('.faa')]) 25 #if $f.endswith('.faa'):
26 set num_orthogroup_faa = $num_orthogroup_faa + 1 26 #set num_orthogroup_faa = $num_orthogroup_faa + 1
27 #end if 27 #end if
28 #end for 28 #end for
29 #if $num_orthogroup_faa == 0: 29 #if $num_orthogroup_faa == 0:
30 print > $sys.stderr($invalid_input) 30 print > $sys.stderr($invalid_input)
31 $sys.exit(1) 31 $sys.exit(1)
32 #end if 32 #end if
33 #set num_orthogroup_fna = 0 33 #set num_orthogroup_fna = 0
34 #for f in $os.listdir($src_dir): 34 #for f in $os.listdir($src_dir):
35 #if $f.endswith('.fna')]) 35 #if $f.endswith('.fna'):
36 set num_orthogroup_fna = $num_orthogroup_fna + 1 36 #set num_orthogroup_fna = $num_orthogroup_fna + 1
37 #end if 37 #end if
38 #end for 38 #end for
39 #set dest_dir = $output.extra_files_path 39 #set dest_dir = $output.extra_files_path
40 mkdir -p $dest_dir && 40 mkdir -p $dest_dir &&
41 PhylogenomicsAnalysis 41 PhylogenomicsAnalysis