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comparison seq_form_db.xml @ 3:46f629f79f55 draft default tip

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planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit e8c8f102cab10531ed588be4ecb8a0d01e797f09
author tduigou
date Tue, 06 Jan 2026 11:48:06 +0000
parents 11a3752feb0a
children
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2:11a3752feb0a 3:46f629f79f55
13 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 mkdir 'outdir' && 14 mkdir 'outdir' &&
15 python '$__tool_directory__/get_db_info.py' 15 python '$__tool_directory__/get_db_info.py'
16 --input '$input' 16 --input '$input'
17 --use_json_paramers '$json_use.use_json_paramers' 17 --use_json_paramers '$json_use.use_json_paramers'
18 #if not $json_use.use_json_paramers: 18 #if $json_use.use_json_paramers=='false':
19 --sequence_column '$json_use.sequence_column' 19 --sequence_column '$json_use.sequence_column'
20 --annotation_columns '$json_use.annotation_columns' 20 --annotation_columns '$json_use.annotation_columns'
21 --db_uri '$json_use.db_uri' 21 --db_uri '$json_use.db_uri'
22 --table '$json_use.table' 22 --table '$json_use.table'
23 --fragment_column '$json_use.fragment_column' 23 --fragment_column '$json_use.fragment_column'
28 --report '$report' 28 --report '$report'
29 ]]></command> 29 ]]></command>
30 <inputs> 30 <inputs>
31 <param name="input" type="data" format="csv" label="Input CSV File" /> 31 <param name="input" type="data" format="csv" label="Input CSV File" />
32 <conditional name="json_use"> 32 <conditional name="json_use">
33 <param name="use_json_paramers" type="boolean" checked='false' label="Use parameters from JSON" help="extract parameters from json file" /> 33 <param name="use_json_paramers" type="select" checked='false' label="Use parameters from JSON" help="extract parameters from json file">
34 <option value="true">Get Parameters From JSON</option>
35 <option value="false" selected="true">Set Parameters Manually</option>
36 </param>
34 <when value="false"> 37 <when value="false">
35 <param name="table" type="text" label="DB Table Name" optional="false" /> 38 <param name="table" type="text" label="DB Table Name" optional="false" />
36 <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="false" /> 39 <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="false" />
37 <param name="annotation_columns" type="text" label="DB Column Contains Annotation For Ganbank File" optional="false" /> 40 <param name="annotation_columns" type="text" label="DB Column Contains Annotation For Ganbank File" optional="false" />
38 <param name="fragment_column" type="text" label="DB IDs Column Name" optional="false" /> 41 <param name="fragment_column" type="text" label="DB IDs Column Name" optional="false" />