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comparison data_manager/checkm2_datamanager.xml @ 4:74c70f37dffb draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit 3e15f64954fb060e11abfe1a6857c21f4032ad9c
author iuc
date Mon, 06 Oct 2025 16:41:35 +0000
parents 6fd780865107
children
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3:6fd780865107 4:74c70f37dffb
1 <tool id="checkm2_build_database" name="CheckM2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="checkm2_build_database" name="CheckM2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>database builder</description> 2 <description>database builder</description>
3 <macros> 3 <macros>
4 <!-- on update run a local test setting `test` to something else than "true" --> 4 <!-- on update run a local test setting `test` to something else than "true" -->
5 <token name="@TOOL_VERSION@">1.0.2</token> 5 <token name="@TOOL_VERSION@">1.1.0</token>
6 <token name="@VERSION_SUFFIX@">1</token> 6 <token name="@VERSION_SUFFIX@">0</token>
7 <token name="@PROFILE@">23.1</token> 7 <token name="@PROFILE@">23.1</token>
8 </macros> 8 </macros>
9 <requirements> 9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">checkm2</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">checkm2</requirement>
11 </requirements> 11 </requirements>
12 <version_command>checkm2 --version</version_command> 12 <version_command>checkm2 --version</version_command>
13 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 mkdir -p '$out_file.extra_files_path' && 14 mkdir -p '$out_file.extra_files_path' &&
15 #if $test != "true" 15 #if $test != "true"
16 wget 'https://zenodo.org/records/5571251/files/checkm2_database.tar.gz' && 16 checkm2 database --download --no_write_json_db --path '$out_file.extra_files_path'/ &&
17 tar -xf 'checkm2_database.tar.gz' -C '$out_file.extra_files_path' &&
18 mv '$out_file.extra_files_path'/CheckM2_database/uniref100.KO.1.dmnd '$out_file.extra_files_path' && 17 mv '$out_file.extra_files_path'/CheckM2_database/uniref100.KO.1.dmnd '$out_file.extra_files_path' &&
19 #else 18 #else
20 touch '$out_file.extra_files_path'/uniref100.KO.1.dmnd && 19 touch '$out_file.extra_files_path'/uniref100.KO.1.dmnd &&
21 #end if 20 #end if
22 cp '$dmjson' '$out_file' 21 cp '$dmjson' '$out_file'