Mercurial > repos > iuc > data_manager_metaphlan_database_downloader
comparison data_manager/data_manager_metaphlan_download.xml @ 6:d8dc037e3c13 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
author | iuc |
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date | Mon, 29 Jul 2024 07:13:31 +0000 |
parents | a88f077f1994 |
children | 2c61c30a57e7 |
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5:a88f077f1994 | 6:d8dc037e3c13 |
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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 '$__tool_directory__/data_manager_metaphlan_download.py' | 15 metaphlan --install --index '$index' --bowtie2db '$out_file.extra_files_path/$index' && |
16 --index '$index' | 16 cp '$dmjson' '$out_file' |
17 --json '$out_file' | |
18 ]]></command> | 17 ]]></command> |
18 <configfiles> | |
19 <configfile name="dmjson"><![CDATA[ | |
20 #from datetime import date | |
21 { | |
22 "data_tables":{ | |
23 "genomad":[ | |
24 { | |
25 "dbkey": "$index", | |
26 "value": "${index}-#echo date.today().strftime('%d%m%Y')#", | |
27 "name": "MetaPhlAn clade-specific marker genes ($index)", | |
28 "path": "$out_file.extra_files_path/$index", | |
29 "db_version": #slurp | |
30 #if "SGB" in str($index) | |
31 "SGB"#slurp | |
32 #else | |
33 "legacy"#slurp | |
34 #end if | |
35 } | |
36 ] | |
37 } | |
38 }]]> | |
39 </configfile> | |
40 </configfiles> | |
19 <inputs> | 41 <inputs> |
20 <param name="index" type="select" label="Version"> | 42 <param name="index" type="select" label="Version"> |
21 <option value="mpa_vOct22_CHOCOPhlAnSGB_202403" selected="true">FULL: mpa_vOct22_CHOCOPhlAnSGB_202403</option> | 43 <option value="mpa_vOct22_CHOCOPhlAnSGB_202403" selected="true">FULL: mpa_vOct22_CHOCOPhlAnSGB_202403</option> |
22 <option value="mpa_vJun23_CHOCOPhlAnSGB_202403" selected="true">FULL: mpa_vJun23_CHOCOPhlAnSGB_202403</option> | 44 <option value="mpa_vJun23_CHOCOPhlAnSGB_202403" selected="true">FULL: mpa_vJun23_CHOCOPhlAnSGB_202403</option> |
23 <option value="mpa_vJun23_CHOCOPhlAnSGB_202307" selected="true">FULL: mpa_vJun23_CHOCOPhlAnSGB_202307</option> | 45 <option value="mpa_vJun23_CHOCOPhlAnSGB_202307" selected="true">FULL: mpa_vJun23_CHOCOPhlAnSGB_202307</option> |
32 <tests> | 54 <tests> |
33 <test expect_num_outputs="1"> | 55 <test expect_num_outputs="1"> |
34 <param name="index" value="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"/> | 56 <param name="index" value="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"/> |
35 <output name="out_file"> | 57 <output name="out_file"> |
36 <assert_contents> | 58 <assert_contents> |
37 <has_text text="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"/> | 59 <has_text text='"db_version": "SGB"'/> |
38 <has_text text="MetaPhlAn clade-specific marker genes (mpa_vJan21_TOY_CHOCOPhlAnSGB_202103)"/> | 60 <has_text text='"dbkey": "mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"'/> |
61 <has_text_matching expression='"value": "mpa_vJan21_TOY_CHOCOPhlAnSGB_202103-[0-9]{8}"'/> | |
62 <has_text text='"name": "MetaPhlAn clade-specific marker genes (mpa_vJan21_TOY_CHOCOPhlAnSGB_202103)"'/> | |
63 <has_text_matching expression='.*"path": ".*/mpa_vJan21_TOY_CHOCOPhlAnSGB_202103".*'/> | |
39 </assert_contents> | 64 </assert_contents> |
40 </output> | 65 </output> |
41 </test> | 66 </test> |
42 </tests> | 67 </tests> |
43 <help><![CDATA[ | 68 <help><![CDATA[ |