Mercurial > repos > iuc > bbtools_bbmerge

comparison bbmerge.xml @ 4:5d8b93c0731f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 8f659e3524ff3fbf70ce9f4090e3fe8a49048b29
author iuc
date Wed, 24 Apr 2024 20:25:07 +0000
parents 82ced0e47b9d
children 1af48f9cc27b
comparison
equal deleted inserted replaced
3:82ced0e47b9d 4:5d8b93c0731f
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="edam_ontology"/> 6 <expand macro="edam_ontology"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 #import os
10 #import re
11
12 #if str($input_type_cond.input_type) in ['single', 'pair']: 9 #if str($input_type_cond.input_type) in ['single', 'pair']:
13 #set read1 = $input_type_cond.read1 10 #set read1 = $input_type_cond.read1
14 ## bbmerge uses the file extension to determine the input format. 11 ## bbmerge uses the file extension to determine the input format.
15 #set ext = '.fastq' 12 #set ext = '.fastq'
16 #if $read1.ext.endswith('.gz'): 13 #if $read1.ext.endswith('.gz'):
23 #set read2_file = 'reverse' + $ext 20 #set read2_file = 'reverse' + $ext
24 ln -s '${read2}' '${read2_file}' && 21 ln -s '${read2}' '${read2_file}' &&
25 #end if 22 #end if
26 #else: 23 #else:
27 #set read1 = $input_type_cond.reads_collection['forward'] 24 #set read1 = $input_type_cond.reads_collection['forward']
28 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
29 ## bbmap uses the file extension to determine the input format. 25 ## bbmap uses the file extension to determine the input format.
30 #set ext = $read1_identifier + '.fastq' 26 #set ext = '.fastq'
31 #if $read1.ext.endswith('.gz'): 27 #if $read1.ext.endswith('.gz'):
32 #set ext = $ext + '.gz' 28 #set ext = $ext + '.gz'
33 #end if 29 #end if
34 #set read1_file = $read1_identifier + $ext 30 #set read1_file = 'forward' + $ext
35 ln -s '${read1}' '${read1_file}' && 31 ln -s '${read1}' '${read1_file}' &&
36 #set read2 = $input_type_cond.reads_collection['reverse'] 32 #set read2 = $input_type_cond.reads_collection['reverse']
37 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) 33 #set read2_file = 'reverse' + $ext
38 #set read2_file = $read2_identifier + $ext
39 ln -s '${read2}' '${read2_file}' && 34 ln -s '${read2}' '${read2_file}' &&
40 #end if 35 #end if
41 36
42 if [[ "\${_JAVA_OPTIONS}" != *-Xmx* && "\${JAVA_TOOL_OPTIONS}" != *-Xmx* ]]; then 37 if [[ "\${_JAVA_OPTIONS}" != *-Xmx* && "\${JAVA_TOOL_OPTIONS}" != *-Xmx* ]]; then
43 export _JAVA_OPTIONS="\${_JAVA_OPTIONS} -Xmx\${GALAXY_MEMORY_MB:-4096}m -Xms256m"; 38 export _JAVA_OPTIONS="\${_JAVA_OPTIONS} -Xmx\${GALAXY_MEMORY_MB:-4096}m -Xms256m";