Mercurial > repos > earlhaminst > lotus2

comparison lotus2.xml @ 11:8f732780e0f3 draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 544a60608fa765463c1d805595a56b8a49a689ea"
author earlhaminst
date Tue, 08 Jun 2021 19:53:13 +0000
parents 6d55d9464719
children 3f3ee496acec
comparison
equal deleted inserted replaced
10:6d55d9464719 11:8f732780e0f3
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, $f_ext): 44 #def symlink_basename($f):
45 #set $fn = re.sub('[^\w\-_.]', '_', $f.element_identifier) 45 #set $fn = re.sub('[^\w\-_.]', '_', $f.name)
46 #if $fn.endswith('.gz'): 46 ${fn}#slurp
47 #set $fn = $fn[:-3]
48 #end if
49 #if $f_ext.startswith('fastq'):
50 #set $exts_to_drop = ('.fq', '.fastq', '.fastqsanger')
51 #elif $f_ext.startswith('fasta'):
52 #set $exts_to_drop = ('.fa', '.fasta', '.fna')
53 #else
54 #set $exts_to_drop = []
55 #end if
56 #for $ext in $exts_to_drop:
57 #if $fn.endswith($ext):
58 #set $fn = $fn[:-len($ext)]
59 #break
60 #end if
61 #end for
62 $fn#slurp
63 #end def 47 #end def
64 48
65 mkdir input 49 mkdir input
66 && 50 &&
67 #if $inputs.paired_or_single == 'single': 51 #if $inputs.paired_or_single == 'single':
68 #for $f in $inputs.input: 52 #for $f in $inputs.input:
69 #set $ext = $f.ext.replace('sanger', '') 53 ln -s '$f' 'input/${symlink_basename($f)}' &&
70 ln -s '$f' 'input/${symlink_basename($f, $ext)}.${ext}' &&
71 #end for
72 #elif $inputs.paired_or_single == 'paired':
73 #for i, f in enumerate($inputs.left_input):
74 #set ext = $f.ext.replace('sanger', '')
75 ln -s '$f' 'input/input${i}.1.${ext}' &&
76 #end for
77 #for $i, $f in enumerate($inputs.right_input):
78 #set $ext = $f.ext.replace('sanger', '')
79 ln -s '$f' 'input/input${i}.2.${ext}' &&
80 #end for 54 #end for
81 #else: 55 #else:
82 #for $f in $inputs.pair_input: 56 #for $f in $inputs.pair_input:
83 #set $ext = $f.forward.ext.replace('sanger', '') 57 ln -s '$f.forward' 'input/${symlink_basename($f.forward.dataset)}' &&
84 ln -s '$f.forward' 'input/${symlink_basename($f, $ext)}.1.${ext}' && 58 ln -s '$f.reverse' 'input/${symlink_basename($f.reverse.dataset)}' &&
85 #set $ext = $f.reverse.ext.replace('sanger', '')
86 ln -s '$f.reverse' 'input/${symlink_basename($f, $ext)}.2.${ext}' &&
87 #end for 59 #end for
88 #end if 60 #end if
89 61
90 #if $tax_args.aligner_cond.taxAligner not in ('0', '3') and $tax_args.aligner_cond.refDB_cond.refDB == 'history': 62 #if $tax_args.aligner_cond.taxAligner not in ('0', '3') and $tax_args.aligner_cond.refDB_cond.refDB == 'history':
91 #set $ext = $tax_args.aligner_cond.refDB_cond.ref_fasta.ext 63 #set $ext = $tax_args.aligner_cond.refDB_cond.ref_fasta.ext
92 #set $ref_fasta_symlink = $symlink_basename($tax_args.aligner_cond.refDB_cond.ref_fasta, $ext) + '.' + $ext 64 #set $ref_fasta_symlink = $symlink_basename($tax_args.aligner_cond.refDB_cond.ref_fasta, $ext) + '.' + $ext
93 ln -s '$tax_args.aligner_cond.refDB_cond.ref_fasta' '$ref_fasta_symlink' && 65 ln -s '$tax_args.aligner_cond.refDB_cond.ref_fasta' '$ref_fasta_symlink' &&
94 #end if 66 #end if
95 67
96 #if not $map: 68 #if not $map:
97 lotus2 -create_map mapping.txt -i input/ && 69 cat '$generated_mapping' &&
98 cat mapping.txt && 70 #set map = $generated_mapping
99 #set map = 'mapping.txt'
100 #end if 71 #end if
101 72
102 lotus2 73 lotus2
103 -i input/ 74 -i input/
104 -o output 75 -o output
190 161
191 zip -8 -r -v output.zip output/ 162 zip -8 -r -v output.zip output/
192 && 163 &&
193 exit \$EXIT_VALUE 164 exit \$EXIT_VALUE
194 ]]></command> 165 ]]></command>
195 166 <configfiles>
167 <configfile name="generated_mapping"><![CDATA[#slurp
168 #import re
169 #def symlink_basename($f):
170 #set $fn = re.sub('[^\w\-_.]', '_', $f.name)
171 ${fn}#slurp
172 #end def
173 #SampleID fastqFile SequencingRun
174 #if $inputs.paired_or_single == 'single':
175 #for $i, $f in enumerate($inputs.input):
176 SMPL${i} ${symlink_basename($f)} a
177 #end for
178 #else:
179 #for $i, $f in enumerate($inputs.pair_input):
180 SMPL${i} ${symlink_basename($f.forward.dataset)},${symlink_basename($f.reverse.dataset)} a
181 #end for
182 #end if
183 ]]></configfile>
184 </configfiles>
196 <inputs> 185 <inputs>
197 <conditional name="inputs"> 186 <conditional name="inputs">
198 <param name="paired_or_single" type="select" label="Single- or Paired-end data?"> 187 <param name="paired_or_single" type="select" label="Single- or Paired-end data?">
199 <option value="single" selected="true">Single-end</option> 188 <option value="single" selected="true">Single-end</option>
200 <option value="paired_collection">Paired-end list</option> 189 <option value="paired_collection">Paired-end list</option>