Mercurial > repos > iuc > bbtools_bbduk

comparison bbduk.xml @ 1:ff3b87a0d205 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
author iuc
date Tue, 01 Feb 2022 22:58:36 +0000
parents 132af91f11b9
children 008b8c6f6b26
comparison
equal deleted inserted replaced
0:132af91f11b9 1:ff3b87a0d205
8 #import os 8 #import os
9 #import re 9 #import re
10 10
11 #if str($input_type_cond.input_type) in ['single', 'pair']: 11 #if str($input_type_cond.input_type) in ['single', 'pair']:
12 #set read1 = $input_type_cond.read1 12 #set read1 = $input_type_cond.read1
13 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
14 ## bbduk uses the file extension to determine the input format. 13 ## bbduk uses the file extension to determine the input format.
15 #set ext = $read1_identifier + '.fastq' 14 #set ext = '.fastq'
16 #if $read1.ext.endswith('.gz'): 15 #if $read1.ext.endswith('.gz'):
17 #set ext = $ext + '.gz' 16 #set ext = $ext + '.gz'
18 #end if 17 #end if
19 #set read1_file = $read1_identifier + $ext 18 #set read1_file = 'forward' + $ext
20 ln -s '${read1}' '${read1_file}' && 19 ln -s '${read1}' '${read1_file}' &&
21 #if str($input_type_cond.input_type) == 'pair': 20 #if str($input_type_cond.input_type) == 'pair':
22 #set read2 = $input_type_cond.read2 21 #set read2 = $input_type_cond.read2
23 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) 22 #set read2_file = 'reverse' + $ext
24 #set read2_file = $read2_identifier + $ext
25 ln -s '${read2}' '${read2_file}' && 23 ln -s '${read2}' '${read2_file}' &&
26 #end if 24 #end if
27 #else: 25 #else:
28 #set read1 = $input_type_cond.reads_collection['forward'] 26 #set read1 = $input_type_cond.reads_collection['forward']
29 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name)) 27 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name))
229 </param> 227 </param>
230 </when> 228 </when>
231 </conditional> 229 </conditional>
232 </inputs> 230 </inputs>
233 <outputs> 231 <outputs>
234 <data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Unmatched)"> 232 <data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Unmatched)">
235 <filter>str(outputs_select).find('outu') >= 0</filter> 233 <filter>str(outputs_select).find('outu') >= 0</filter>
236 <filter>'outu' in outputs_select</filter> 234 <filter>'outu' in outputs_select</filter>
237 </data> 235 </data>
238 <data name="outputu2" format="fastqsanger" label="${tool.name} on ${on_string} (Unmatched)"> 236 <data name="outputu2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Unmatched)">
239 <filter>'outu' in outputs_select and input_type_cond['input_type'] != 'single'</filter> 237 <filter>'outu' in outputs_select and input_type_cond['input_type'] != 'single'</filter>
240 </data> 238 </data>
241 <data name="outputm" format="fastqsanger" label="${tool.name} on ${on_string} (Matched)"> 239 <data name="outputm" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Matched)">
242 <filter>'outm' in outputs_select</filter> 240 <filter>'outm' in outputs_select</filter>
243 </data> 241 </data>
244 <data name="outputm2" format="fastqsanger" label="${tool.name} on ${on_string} (Matched)"> 242 <data name="outputm2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Matched)">
245 <filter>'outm' in outputs_select and input_type_cond['input_type'] != 'single'</filter> 243 <filter>'outm' in outputs_select and input_type_cond['input_type'] != 'single'</filter>
246 </data> 244 </data>
247 <data name="outputs" format="fastqsanger" label="${tool.name} on ${on_string} (Single)"> 245 <data name="outputs" format="fastqsanger" label="${tool.name} on ${on_string} (Single)">
248 <filter>'outs' in outputs_select</filter> 246 <filter>'outs' in outputs_select</filter>
249 </data> 247 </data>