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comparison sbol_converter.xml @ 5:35be791462c2 draft default tip

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planemo upload for repository https://github.com/SynBioDex/SBOL-utilities commit f7df6238cbaa188a138cb48217658b6c7b22a181
author tduigou
date Mon, 05 Jun 2023 09:31:26 +0000
parents 5814c9ffbdef
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4:5814c9ffbdef 5:35be791462c2
8 <requirement type="package" version="@TOOL_VERSION@">sbol-utilities</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">sbol-utilities</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 #if str($convert_type.type) == "SBOL2 to SBOL3" 11 #if str($convert_type.type) == "SBOL2 to SBOL3"
12 ln -sv '$sbol2_input' 'input.$sbol2_input.ext' && 12 ln -sv '$sbol2_input' 'input.$sbol2_input.ext' &&
13 sbol2to3 -o '$output' 'input.$sbol2_input.ext' 13 sbol2-to-sbol3 -o '$output' 'input.$sbol2_input.ext'
14 #elif str($convert_type.type) == "SBOL3 to SBOL2" 14 #elif str($convert_type.type) == "SBOL3 to SBOL2"
15 ln -sv '$sbol3_input' 'input.$sbol3_input.ext' && 15 ln -sv '$sbol3_input' 'input.$sbol3_input.ext' &&
16 sbol3to2 -o '$output' 'input.$sbol3_input.ext' 16 sbol3-to-sbol2 -o '$output' 'input.$sbol3_input.ext'
17 #elif str($convert_type.type) == "SBOL3 to GENBANK" 17 #elif str($convert_type.type) == "SBOL3 to GENBANK"
18 ln -sv '$sbol3_input' 'input.$sbol3_input.ext' && 18 ln -sv '$sbol3_input' 'input.$sbol3_input.ext' &&
19 sbol2genbank -o '$output' 'input.$sbol3_input.ext' 19 sbol-to-genbank -o '$output' 'input.$sbol3_input.ext'
20 #elif str($convert_type.type) == "GENBANK to SBOL3" 20 #elif str($convert_type.type) == "GENBANK to SBOL3"
21 ln -sv '$genbank_input' 'input.$genbank_input.ext' && 21 ln -sv '$genbank_input' 'input.$genbank_input.ext' &&
22 genbank2sbol -o '$output' 'input.$genbank_input.ext' --namespace '$convert_type.namespace' 22 genbank-to-sbol -o '$output' 'input.$genbank_input.ext' --namespace '$convert_type.namespace'
23 #elif str($convert_type.type) == "SBOL3 to FASTA" 23 #elif str($convert_type.type) == "SBOL3 to FASTA"
24 ln -sv '$sbol3_input' 'input.$sbol3_input.ext' && 24 ln -sv '$sbol3_input' 'input.$sbol3_input.ext' &&
25 sbol2fasta -o '$output' 'input.$sbol3_input.ext' 25 sbol-to-fasta -o '$output' 'input.$sbol3_input.ext'
26 #elif str($convert_type.type) == "FASTA to SBOL3" 26 #elif str($convert_type.type) == "FASTA to SBOL3"
27 ln -sv '$fasta_input' 'input.$fasta_input.ext' && 27 ln -sv '$fasta_input' 'input.$fasta_input.ext' &&
28 fasta2sbol -o '$output' 'input.$fasta_input.ext' --namespace '$convert_type.namespace' 28 fasta-to-sbol -o '$output' 'input.$fasta_input.ext' --namespace '$convert_type.namespace'
29 #elif str($convert_type.type) == "SBOL2 to FASTA" 29 #elif str($convert_type.type) == "SBOL2 to FASTA"
30 ln -sv '$sbol2_input' 'input.$sbol2_input.ext' && 30 ln -sv '$sbol2_input' 'input.$sbol2_input.ext' &&
31 sbol-converter SBOL2 FASTA -o '$output' 'input.$sbol2_input.ext' 31 sbol-converter SBOL2 FASTA -o '$output' 'input.$sbol2_input.ext'
32 #elif str($convert_type.type) == "FASTA to SBOL2" 32 #elif str($convert_type.type) == "FASTA to SBOL2"
33 ln -sv '$fasta_input' 'input.$fasta_input.ext' && 33 ln -sv '$fasta_input' 'input.$fasta_input.ext' &&