Mercurial > repos > iuc > data_manager_metaphlan_database_downloader
diff 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 |
---|---|
date | Mon, 29 Jul 2024 07:13:31 +0000 |
parents | a88f077f1994 |
children | 2c61c30a57e7 |
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--- a/data_manager/data_manager_metaphlan_download.xml Fri Jun 14 21:14:55 2024 +0000 +++ b/data_manager/data_manager_metaphlan_download.xml Mon Jul 29 07:13:31 2024 +0000 @@ -12,10 +12,32 @@ <exit_code range="1:" level="fatal" description="Error"/> </stdio> <command><![CDATA[ -python '$__tool_directory__/data_manager_metaphlan_download.py' - --index '$index' - --json '$out_file' + metaphlan --install --index '$index' --bowtie2db '$out_file.extra_files_path/$index' && + cp '$dmjson' '$out_file' ]]></command> + <configfiles> + <configfile name="dmjson"><![CDATA[ +#from datetime import date +{ + "data_tables":{ + "genomad":[ + { + "dbkey": "$index", + "value": "${index}-#echo date.today().strftime('%d%m%Y')#", + "name": "MetaPhlAn clade-specific marker genes ($index)", + "path": "$out_file.extra_files_path/$index", + "db_version": #slurp +#if "SGB" in str($index) +"SGB"#slurp +#else +"legacy"#slurp +#end if + } + ] + } +}]]> + </configfile> + </configfiles> <inputs> <param name="index" type="select" label="Version"> <option value="mpa_vOct22_CHOCOPhlAnSGB_202403" selected="true">FULL: mpa_vOct22_CHOCOPhlAnSGB_202403</option> @@ -34,8 +56,11 @@ <param name="index" value="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"/> <output name="out_file"> <assert_contents> - <has_text text="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"/> - <has_text text="MetaPhlAn clade-specific marker genes (mpa_vJan21_TOY_CHOCOPhlAnSGB_202103)"/> + <has_text text='"db_version": "SGB"'/> + <has_text text='"dbkey": "mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"'/> + <has_text_matching expression='"value": "mpa_vJan21_TOY_CHOCOPhlAnSGB_202103-[0-9]{8}"'/> + <has_text text='"name": "MetaPhlAn clade-specific marker genes (mpa_vJan21_TOY_CHOCOPhlAnSGB_202103)"'/> + <has_text_matching expression='.*"path": ".*/mpa_vJan21_TOY_CHOCOPhlAnSGB_202103".*'/> </assert_contents> </output> </test>