Mercurial > repos > thanhlv > data_manager_build_ariba_database
diff data_manager/ariba_database_builder.xml.bk @ 0:a8bb47cc7625 draft
planemo upload for repository tbd commit 0af229dbbda0496819ca95938c2e0628db689134
| author | thanhlv |
|---|---|
| date | Tue, 08 Jan 2019 11:04:25 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/ariba_database_builder.xml.bk Tue Jan 08 11:04:25 2019 -0500 @@ -0,0 +1,41 @@ +<?xml version="1.0"?> +<tool id="ariba_database_builder" name="ARIBA build database" tool_type="manage_data" version="@VERSION@"> + <description>database builder</description> + <expand macro="requirements" /> + <version_command>ariba version | head head -n 1</version_command> + <command detect_errors="exit_code"> + <![CDATA[ + #set $library_list = str($libraries).split(',') + mkdir ariba-database && cd ariba-database && + #for $library in $library_list: + #if str($library) != 'None': + ariba getref $library _tmp_db && ariba prepareref -f _tmp_db.fa -m _tmp_db.tsv $library && + #end if + #end for + #for $fasta in $input_fasta: + #if str($fasta) != 'None': + ariba preparef --all_coding no $fasta $fasta && + #end if + #end for + cd .. && + python '$__tool_directory__/ariba_data_base_builder.py' --db '${database_name}' --out '${out_file}' + ]]> + </command> + <inputs> + <param name="database_name" type="text" label="Name for this database" /> + <param name="libraries" type="select" multiple="true" label="Select partial library to download"> + <option value="card">CARD</option> + <option value="resfinder">Resfinder</option> + <option value="plasmidfinder">Plasmidfinder</option> + </param> + <param name="input_fasta" type="data" format="fasta" multiple="True" optional="true" label="Select history item" /> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" /> + </outputs> + <help> + </help> + <citations> + <citation type="doi">110.1099/mgen.0.000131</citation> + </citations> +</tool>