Mercurial > repos > earlhaminst > lotus2

comparison lotus2.xml @ 12:3f3ee496acec draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e49cb599d171a596ba6a04f73f651e46ac2e4e8a"
author earlhaminst
date Wed, 09 Jun 2021 15:55:53 +0000
parents 8f732780e0f3
children f2bb89058e99
comparison
equal deleted inserted replaced
11:8f732780e0f3 12:3f3ee496acec
39 </requirements> 39 </requirements>
40 <version_command>lotus2 --version</version_command> 40 <version_command>lotus2 --version</version_command>
41 <command detect_errors="exit_code"><![CDATA[ 41 <command detect_errors="exit_code"><![CDATA[
42 #import os.path 42 #import os.path
43 #import re 43 #import re
44 #def symlink_basename($f): 44 #def symlink_basename($f, strip_ext=False):
45 #set $fn = re.sub('[^\w\-_.]', '_', $f.name) 45 #set $fn = re.sub('[^\w\-_.]', '_', $f.name)
46 #if strip_ext:
47 #if $fn.endswith('.gz'):
48 #set $fn = $fn[:-3]
49 #end if
50 #if $f.ext.startswith('fasta'):
51 #set $exts_to_drop = ('.fa', '.fasta', '.fna')
52 #else:
53 #set $exts_to_drop = []
54 #end if
55 #for $ext in $exts_to_drop:
56 #if $fn.endswith($ext):
57 #set $fn = $fn[:-len($ext)]
58 #break
59 #end if
60 #end for
61 #end if
46 ${fn}#slurp 62 ${fn}#slurp
47 #end def 63 #end def
48 64
49 mkdir input 65 mkdir input
50 && 66 &&
59 #end for 75 #end for
60 #end if 76 #end if
61 77
62 #if $tax_args.aligner_cond.taxAligner not in ('0', '3') and $tax_args.aligner_cond.refDB_cond.refDB == 'history': 78 #if $tax_args.aligner_cond.taxAligner not in ('0', '3') and $tax_args.aligner_cond.refDB_cond.refDB == 'history':
63 #set $ext = $tax_args.aligner_cond.refDB_cond.ref_fasta.ext 79 #set $ext = $tax_args.aligner_cond.refDB_cond.ref_fasta.ext
64 #set $ref_fasta_symlink = $symlink_basename($tax_args.aligner_cond.refDB_cond.ref_fasta, $ext) + '.' + $ext 80 #set $ref_fasta_symlink = $symlink_basename($tax_args.aligner_cond.refDB_cond.ref_fasta, strip_ext=True) + '.' + $ext
65 ln -s '$tax_args.aligner_cond.refDB_cond.ref_fasta' '$ref_fasta_symlink' && 81 ln -s '$tax_args.aligner_cond.refDB_cond.ref_fasta' '$ref_fasta_symlink' &&
66 #end if 82 #end if
67 83
68 #if not $map: 84 #if not $map:
69 cat '$generated_mapping' && 85 cat '$generated_mapping' &&