Mercurial > repos > iuc > data_manager_metaphlan_database_downloader
view data_manager/data_manager_metaphlan_download.xml @ 6:d8dc037e3c13 draft default tip
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 |
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<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"> <description></description> <macros> <token name="@TOOL_VERSION@">4.0.6</token> <token name="@VERSION_SUFFIX@">3</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">metaphlan</requirement> </requirements> <stdio> <exit_code range=":-1" level="fatal" description="Error: Cannot open file"/> <exit_code range="1:" level="fatal" description="Error"/> </stdio> <command><![CDATA[ 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($index) "SGB"#slurp #else "legacy"#slurp #end if } ] } }]]> </configfile> </configfiles> <inputs> <param name="index" type="select" label="Version"> <option value="mpa_vOct22_CHOCOPhlAnSGB_202403" selected="true">FULL: mpa_vOct22_CHOCOPhlAnSGB_202403</option> <option value="mpa_vJun23_CHOCOPhlAnSGB_202403" selected="true">FULL: mpa_vJun23_CHOCOPhlAnSGB_202403</option> <option value="mpa_vJun23_CHOCOPhlAnSGB_202307" selected="true">FULL: mpa_vJun23_CHOCOPhlAnSGB_202307</option> <option value="mpa_vOct22_CHOCOPhlAnSGB_202212" selected="true">FULL: mpa_vOct22_CHOCOPhlAnSGB_202212</option> <option value="mpa_vJan21_CHOCOPhlAnSGB_202103">FULL: mpa_vJan21_CHOCOPhlAnSGB_202103</option> <option value="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103">DEMO: mpa_vJan21_TOY_CHOCOPhlAnSGB_202103</option> </param> </inputs> <outputs> <data name="out_file" format="data_manager_json" label="${tool.name}"/> </outputs> <tests> <test expect_num_outputs="1"> <param name="index" value="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"/> <output name="out_file"> <assert_contents> <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> </tests> <help><![CDATA[ This tool downloads and builds the MetaPhlAn databases. ]]></help> <citations> <citation type="doi">1101/2020.11.19.388223</citation> </citations> </tool>