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comparison malt_run.xml @ 1:d9b0eda57c0b draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt commit 6bde7c9985265b3086f1e1a6df814c20d02ee092"
author iuc
date Mon, 09 May 2022 15:07:25 +0000
parents 0f45b98a5a08
children
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0:0f45b98a5a08 1:d9b0eda57c0b
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #import re 8 #import re
9
10 ## This will point to a directory.
11 #set ref = str($reference.fields.path)
12 9
13 #set input_identifier = re.sub('[^\s\w\-]', '_', str($input.element_identifier)) 10 #set input_identifier = re.sub('[^\s\w\-]', '_', str($input.element_identifier))
14 ## malt-run uses the file extension to determine the input format. 11 ## malt-run uses the file extension to determine the input format.
15 #if $input.is_of_type('fasta', 'fasta.gz'): 12 #if $input.is_of_type('fasta', 'fasta.gz'):
16 #set input_identifier = $input_identifier + '.fasta' 13 #set input_identifier = $input_identifier + '.fasta'
40 $mode_cond.reverse_only 37 $mode_cond.reverse_only
41 #end if 38 #end if
42 39
43 --alignmentType '$alignmentType' 40 --alignmentType '$alignmentType'
44 --inFile '$input_identifier' 41 --inFile '$input_identifier'
45 --index '$ref' 42 --index '$reference.fields.path'
46 ## malt-run requires correct output file extensions. 43 ## malt-run requires correct output file extensions.
47 --output './output.rma6' 44 --output './output.rma6'
48 --numThreads \${GALAXY_SLOTS:-12} 45 --numThreads \${GALAXY_SLOTS:-12}
49 46
50 --memoryMode '$advanced_options_performance.memoryMode' 47 --memoryMode '$advanced_options_performance.memoryMode'