Mercurial > repos > iuc > checkm2_build_database
comparison data_manager/checkm2_datamanager.xml @ 2:df2f47a0e57a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit 2ae2ddbe15eb071a70355aa0738d753e8d2cdc2e
author | iuc |
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date | Wed, 19 Feb 2025 13:53:53 +0000 |
parents | 64630d815957 |
children |
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1:64630d815957 | 2:df2f47a0e57a |
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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@">1.0.2</token> |
6 <token name="@VERSION_SUFFIX@">0</token> | 6 <token name="@VERSION_SUFFIX@">1</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 $test != "true" |
16 checkm2 database --download --path '$out_file.extra_files_path'/ && | 16 wget 'https://zenodo.org/records/5571251/files/checkm2_database.tar.gz' && |
17 tar -xf 'checkm2_database.tar.gz' -C '$out_file.extra_files_path' && | |
17 mv '$out_file.extra_files_path'/CheckM2_database/uniref100.KO.1.dmnd '$out_file.extra_files_path' && | 18 mv '$out_file.extra_files_path'/CheckM2_database/uniref100.KO.1.dmnd '$out_file.extra_files_path' && |
18 #else | 19 #else |
19 touch '$out_file.extra_files_path'/uniref100.KO.1.dmnd && | 20 touch '$out_file.extra_files_path'/uniref100.KO.1.dmnd && |
20 #end if | 21 #end if |
21 cp '$dmjson' '$out_file' | 22 cp '$dmjson' '$out_file' |