Mercurial > repos > rhpvorderman > data_manager_select_index_by_path
comparison 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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1 <tool id="data_manager_select_index_by_path" name="Select index by path manager" tool_type="manage_data" version="0.0.2"> | |
2 <description>path inputer</description> | |
3 <command interpreter="python"> | |
4 path_name_value_key_manager.py | |
5 --value "${value}" | |
6 --dbkey "${dbkey}" | |
7 --name "${name}" | |
8 --path "${path}" | |
9 --data_table_name "${data_table}" | |
10 --json_output_file "${json_output_file}" | |
11 </command> | |
12 <inputs> | |
13 <param name="value" type="text" value="" label="value field for the entry. Defaults to name if left blank." /> | |
14 <param name="dbkey" type="text" value="" label="dbkey field for the entry. Defaults to value if left blank." /> | |
15 <param name="name" type="text" value="" label="name field for the entry. Defaults to the file name from path if left blank." /> | |
16 <param name="path" type="text" value="" label="path field for the entry" /> | |
17 <param name="data_table" type="select" value="" label="data table for the index"> | |
18 <option value='all_fasta'>all_fasta</option> | |
19 <option value='bowtie2_indexes'>bowtie2_indexes</option> | |
20 <option value='bowtie_indexes'>bowtie_indexes</option> | |
21 <option value='bowtie_indexes_color'>bowtie_indexes_color</option> | |
22 <option value='bwa_mem_indexes'>bwa_mem_indexes</option> | |
23 <option value='bwameth_indexes'>bwameth_indexes</option> | |
24 <option value='fasta_indexes'>fasta_indexes</option> | |
25 <option value='gatk_picard_indexes'>gatk_picard_indexes</option> | |
26 <option value='gene_transfer'>gene_transfer</option> | |
27 <option value='hisat2_indexes'>hisat2_indexes</option> | |
28 <option value='kallisto_indexes'>kallisto_indexes</option> | |
29 <option value='picard_indexes'>picard_indexes</option> | |
30 <option value='tophat2_indexes'>tophat2_indexes</option> | |
31 </param> | |
32 </inputs> | |
33 <outputs> | |
34 <data name="json_output_file" format="data_manager_json"/> | |
35 </outputs> | |
36 | |
37 <help> | |
38 Adds a server path to the selected data table. | |
39 | |
40 The tool will check the path exists but NOT check that it holds the expected data type. | |
41 | |
42 If name is not provided the filename from path less the extension is used. | |
43 | |
44 If value is not provided, the name will be used (or its default) | |
45 | |
46 If dbkey is not provided, the value will be used (or its default) | |
47 | |
48 </help> | |
49 <citations> | |
50 </citations> | |
51 | |
52 </tool> |