Mercurial > repos > iuc > data_manager_metaphlan_database_downloader
comparison data_manager/data_manager_metaphlan_download.xml @ 2:5fe20c915fa6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
author | iuc |
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date | Tue, 28 Mar 2023 18:54:12 +0000 |
parents | 9c43baa60906 |
children | 4ba60cb14cb0 |
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1:9c43baa60906 | 2:5fe20c915fa6 |
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1 <tool id="data_manager_metaphlan_download" name="Download and build MetaPhlAn database" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01"> | 1 <tool id="data_manager_metaphlan_download" name="Download and build MetaPhlAn database" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="22.05"> |
2 <description></description> | 2 <description></description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="@TOOL_VERSION@">metaphlan</requirement> | 4 <requirement type="package" version="@TOOL_VERSION@">metaphlan</requirement> |
5 </requirements> | 5 </requirements> |
6 <macros> | 6 <macros> |
7 <token name="@TOOL_VERSION@">3.0.7</token> | 7 <token name="@TOOL_VERSION@">4.0.6</token> |
8 <token name="@VERSION_SUFFIX@">0</token> | 8 <token name="@VERSION_SUFFIX@">0</token> |
9 </macros> | 9 </macros> |
10 <stdio> | 10 <stdio> |
11 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | 11 <exit_code range=":-1" level="fatal" description="Error: Cannot open file"/> |
12 <exit_code range="1:" level="fatal" description="Error" /> | 12 <exit_code range="1:" level="fatal" description="Error"/> |
13 </stdio> | 13 </stdio> |
14 <command><![CDATA[ | 14 <command><![CDATA[ |
15 python '$__tool_directory__/data_manager_metaphlan_download.py' | 15 python '$__tool_directory__/data_manager_metaphlan_download.py' |
16 --index '$index' | 16 --index '$index' |
17 --json '$out_file' | 17 --json '$out_file' |
18 ]]></command> | 18 ]]></command> |
19 <inputs> | 19 <inputs> |
20 <param name="index" type="select" label="Version"> | 20 <param name="index" type="select" label="Version"> |
21 <option value="mpa_v30_CHOCOPhlAn_201901" selected="true">mpa_v30_CHOCOPhlAn_201901</option> | 21 <option value="mpa_vOct22_CHOCOPhlAnSGB_202212" selected="true">mpa_vOct22_CHOCOPhlAnSGB_202212</option> |
22 <option value="mpa_vJan21_CHOCOPhlAnSGB_202103">mpa_vJan21_CHOCOPhlAnSGB_202103</option> | |
22 </param> | 23 </param> |
23 </inputs> | 24 </inputs> |
24 <outputs> | 25 <outputs> |
25 <data name="out_file" format="data_manager_json" label="${tool.name}"/> | 26 <data name="out_file" format="data_manager_json" label="${tool.name}"/> |
26 </outputs> | 27 </outputs> |
27 <tests> | 28 <tests> |
28 <test expect_num_outputs="1"> | 29 <!-- |
29 <param name="index" value="mpa_v30_CHOCOPhlAn_201901"/> | 30 <test expect_num_outputs="1"> |
30 <output name="out_file"> | 31 <param name="index" value="mpa_vOct22_CHOCOPhlAnSGB_202212"/> |
31 <assert_contents> | 32 <output name="out_file"> |
32 <has_text text="mpa_v30_CHOCOPhlAn_201901-"/> | 33 <assert_contents> |
33 <has_text text="MetaPhlAn clade-specific marker genes (mpa_v30_CHOCOPhlAn_201901)"/> | 34 <has_text text="mpa_vOct22_CHOCOPhlAnSGB_202212"/> |
34 </assert_contents> | 35 <has_text text="MetaPhlAn clade-specific marker genes (mpa_vOct22_CHOCOPhlAnSGB_202212)"/> |
35 </output> | 36 </assert_contents> |
36 </test> | 37 </output> |
38 </test> | |
39 --> | |
37 </tests> | 40 </tests> |
38 <help><![CDATA[ | 41 <help><![CDATA[ |
39 This tool downloads and builds the MetaPhlAn databases. | 42 This tool downloads and builds the MetaPhlAn databases. |
40 ]]></help> | 43 ]]></help> |
41 <citations> | 44 <citations> |