Mercurial > repos > iuc > malt_run
comparison malt_run.xml @ 1:87a1202c03e8 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt commit 6bde7c9985265b3086f1e1a6df814c20d02ee092"
author | iuc |
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date | Mon, 09 May 2022 15:08:00 +0000 |
parents | d505990b8c89 |
children |
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0:d505990b8c89 | 1:87a1202c03e8 |
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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' |