Mercurial > repos > rhpvorderman > data_manager_select_index_by_path
diff data_manager/data_manager_select_index_by_path.xml @ 0:5f8d9309058b draft
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
author | rhpvorderman |
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date | Mon, 25 Sep 2017 03:35:26 -0400 |
parents | |
children | 8495c49cd056 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_select_index_by_path.xml Mon Sep 25 03:35:26 2017 -0400 @@ -0,0 +1,52 @@ +<tool id="data_manager_select_index_by_path" name="Select index by path manager" tool_type="manage_data" version="0.0.2"> + <description>path inputer</description> + <command interpreter="python"> + path_name_value_key_manager.py + --value "${value}" + --dbkey "${dbkey}" + --name "${name}" + --path "${path}" + --data_table_name "${data_table}" + --json_output_file "${json_output_file}" + </command> + <inputs> + <param name="value" type="text" value="" label="value field for the entry. Defaults to name if left blank." /> + <param name="dbkey" type="text" value="" label="dbkey field for the entry. Defaults to value if left blank." /> + <param name="name" type="text" value="" label="name field for the entry. Defaults to the file name from path if left blank." /> + <param name="path" type="text" value="" label="path field for the entry" /> + <param name="data_table" type="select" value="" label="data table for the index"> + <option value='all_fasta'>all_fasta</option> + <option value='bowtie2_indexes'>bowtie2_indexes</option> + <option value='bowtie_indexes'>bowtie_indexes</option> + <option value='bowtie_indexes_color'>bowtie_indexes_color</option> + <option value='bwa_mem_indexes'>bwa_mem_indexes</option> + <option value='bwameth_indexes'>bwameth_indexes</option> + <option value='fasta_indexes'>fasta_indexes</option> + <option value='gatk_picard_indexes'>gatk_picard_indexes</option> + <option value='gene_transfer'>gene_transfer</option> + <option value='hisat2_indexes'>hisat2_indexes</option> + <option value='kallisto_indexes'>kallisto_indexes</option> + <option value='picard_indexes'>picard_indexes</option> + <option value='tophat2_indexes'>tophat2_indexes</option> + </param> + </inputs> + <outputs> + <data name="json_output_file" format="data_manager_json"/> + </outputs> + + <help> +Adds a server path to the selected data table. + +The tool will check the path exists but NOT check that it holds the expected data type. + +If name is not provided the filename from path less the extension is used. + +If value is not provided, the name will be used (or its default) + +If dbkey is not provided, the value will be used (or its default) + + </help> + <citations> + </citations> + +</tool>