Mercurial > repos > blankenberglab > data_manager_refgenie_pull
view data_manager/data_manager_refgenie_pull.xml @ 5:0445344b7c3f draft default tip
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
author | blankenberglab |
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date | Fri, 01 Apr 2022 16:02:32 +0000 |
parents | f80b9af92d97 |
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<tool id="data_manager_refgenie_pull" name="refgenie asset pulling" version="@VERSION@+galaxy0" tool_type="manage_data" profile="20.05"> <description>from remote resource</description> <macros> <import>macros.xml</import> </macros> <requirements> <requirement type="package" version="@VERSION@">refgenie</requirement> </requirements> <version_command>refgenie --version</version_command> <code file="data_manager_refgenie_pull.py" /> <environment_variables> <environment_variable name="API_KEY" inject="api_key" /> </environment_variables> <command detect_errors="exit_code"><![CDATA[ #for $asset in $assets: #set ga = str($asset).split('/',2) refgenie pull -c '$__app__.config.refgenie_config_file' -g '$ga[1]' '$ga[2]' $force >> '${out_log}' 2>&1 && #end for echo '{}' > '${out_file}' #if "refresh" in $str($api_refresh): && python '${__tool_directory__}/data_manager_refgenie_pull.py' -k "\$API_KEY" -u '${__galaxy_url__}' #if "graceful" in $str($api_refresh): --graceful #end if >> '${out_log}' #end if ]]></command> <inputs> <param argument="--assets" name="assets" type="drill_down" display="checkbox" hierarchy="exact" multiple="True" optional="False" label="Select desired asset" dynamic_options="galaxy_code_get_refgenie_assets(__trans__.app.config.refgenie_config_file)" help="string of asset-registry-paths"> <validator type="regex" message="You must select an asset, not the remote URL or genome.">.+/.+/.+</validator> </param> <param argument="--force" name="force" type="boolean" truevalue="--force" falsevalue="" checked="False" label="Force (re-)download" /> <param name="api_refresh" type="select" label="Refresh Galaxy data tables using API" help="Refresh gracefully will attempt to refresh, but a failure will not be fatal."> <option value="refresh">Refresh</option> <option value="refresh_graceful" selected="True">Refresh gracefully</option> <option value="no">Do not refresh</option> </param> </inputs> <outputs> <data name="out_file" format="data_manager_json" label="${tool.name}: data manager json"/> <data name="out_log" format="txt" label="${tool.name}: log file"/> </outputs> <tests> <test> <param name="assets" value="aHR0cDovL3JlZmdlbm9tZXMuZGF0YWJpby5vcmcvdjIvYXNzZXRz/t7/fasta:default"/> <param name="force" value="--force"/> <param name="api_refresh" value="no"/> <output name="out_file"> <assert_contents> <has_text text="{}"/> </assert_contents> </output> <output name="out_log"> <assert_contents> <has_text text="Download complete"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ **What it does** Fetches a reference genome using refgenie (http://refgenie.databio.org). .. class:: infomark **Notice:** Galaxy data tables will be refreshed using API calls. You must have configured Galaxy to work with refgenie, see https://galaxyproject.org/admin/refgenie/. .. class:: warning **You must configure Galaxy to use refgenie, by setting 'refgenie_config_file' in the Galaxy config. This tool uses refgenie config file version 0.4.** ]]></help> <citations> <citation type="doi">10.1093/gigascience/giz149</citation> <citation type="doi">10.1101/2020.10.09.327114</citation> </citations> </tool>