Mercurial > repos > brenninc > data_manager_for_directory_data
comparison data_manager/directory_data_manager.xml @ 0:43083927dfc5 draft default tip
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author | brenninc |
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date | Sat, 07 May 2016 16:59:47 -0400 |
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-1:000000000000 | 0:43083927dfc5 |
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1 <tool id="directory_data_manager" name="directory data manager" tool_type="manage_data" version="0.0.1"> | |
2 <description>path inputer</description> | |
3 <command interpreter="python"> | |
4 directory_data_manager.py | |
5 --data_table_name "directory_data" | |
6 --json_output_file "${json_output_file}" | |
7 </command> | |
8 <inputs> | |
9 <param name="path" type="text" value="" label="path field for the entry" /> | |
10 <param name="original_extension" type="text" value="" label="Extensions as found in directory." /> | |
11 <param name="galaxy_extension" type="text" value="" label="Galaxay Extension." /> | |
12 <param name="decompress" type="select" label="Will files need to be decompressed."> | |
13 <option value="Yes">Yes. Files should decompressed (unzipped)</option> | |
14 <option value="No">No. Files are not compressed</option> | |
15 </param> | |
16 <param name="value" type="text" value="" label="value field for the entry. Defaults to name if left blank." /> | |
17 <param name="dbkey" type="text" value="" label="dbkey field for the entry. Defaults to value if left blank." /> | |
18 <param name="name" type="text" value="" label="name field for the entry. Defaults to the file name from path if left blank." /> | |
19 </inputs> | |
20 <outputs> | |
21 <data name="json_output_file" format="data_manager_json"/> | |
22 </outputs> | |
23 | |
24 <help> | |
25 Adds information for downloading data to the directory_data data table. | |
26 | |
27 Reguried inputs | |
28 =============== | |
29 | |
30 path | |
31 ---- | |
32 | |
33 Full path on the server where galaxy can find the files | |
34 | |
35 Original Extension | |
36 ------------------ | |
37 | |
38 The Extention as found on the server. | |
39 | |
40 Parts before the extension that could be used to split the data into seubsection such are Read1 and Read2 should not e included. | |
41 | |
42 Galaxy_Extension | |
43 ---------------- | |
44 | |
45 The Extention to give the file before loading into galaxy so galaxy can detect the file type. | |
46 | |
47 This should be one as listed in galaxy/config/datatypes_conf.xml (or xml.sample) | |
48 | |
49 For example use tabular for tsv, txt for text and fasta and not fa\n | |
50 | |
51 Ideally use fastqsanger, fastqsolexa, fastqcssanger, or fastqillumina instead of just fastq as many tools need this level of detail. | |
52 | |
53 Decompress | |
54 ---------- | |
55 | |
56 'Yes' to ask the tool to decompress the files otherwise 'No'. | |
57 | |
58 Any other value will cause an error. | |
59 | |
60 Optional Inputs | |
61 =============== | |
62 | |
63 Name | |
64 ---- | |
65 | |
66 If not provided the last bit of **path** is used. | |
67 | |
68 Value | |
69 ----- | |
70 | |
71 If value is not provided, the **name** will be used (or its default) | |
72 | |
73 dbkey | |
74 ----- | |
75 | |
76 If not provided, the **value** will be used (or its default) | |
77 | |
78 === | |
79 | |
80 The tool will check the path exists and that it holds at least one file with the required extension. | |
81 | |
82 </help> | |
83 <citations> | |
84 </citations> | |
85 | |
86 </tool> |