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comparison rgi.xml @ 4:ce852ee2c394 draft

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planemo upload for repository https://github.com/arpcard/rgi commit 78185f967f4c08824f0b118214adcecc14495f3e
author card
date Wed, 31 Aug 2022 01:14:48 +0000
parents a671367c326e
children 84bd24ac33fd
comparison
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3:bfbfc24c5af2 4:ce852ee2c394
1 <tool id="rgi" name="Resistance Gene Identifier (RGI)" version="5.1.1"> 1 <tool id="rgi" name="Resistance Gene Identifier (RGI)" version="5.2.1">
2 <description>This tool predicts resistome(s) from protein or nucleotide data based on homology and SNP models.</description> 2 <description>This tool predicts resistome(s) from protein or nucleotide data based on homology and SNP models.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="5.1.1">rgi</requirement> 4 <requirement type="package" version="5.2.1">rgi</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" /> 7 <exit_code range="1:" />
8 </stdio> 8 </stdio>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 #if $db_opts.db_opts_selector == "default":
11 export DB_PATH='${__tool_data_path__}/rgi_databases/_default' &&
12 export DATA_PATH="\$_GALAXY_JOB_TMP_DIR" &&
13 mkdir -p "\$DB_PATH" &&
14 #end if
15
10 #if $db_opts.db_opts_selector != "default": 16 #if $db_opts.db_opts_selector != "default":
11 rgi load 17 rgi load
12 #if $db_opts.db_opts_selector == "local": 18 #if $db_opts.db_opts_selector == "local":
13 -i "${__tool_data_path__}/rgi_databases/$db_opts.rgi_db_local/card.json" 19 -i "${__tool_data_path__}/rgi_databases/$db_opts.rgi_db_local/card.json"
14 #else: 20 #else: