Mercurial > repos > bgruening > data_manager_diamond_database_builder
comparison data_manager/data_manager_diamond_database_builder.xml @ 0:ce62d0912b10 draft
Imported from capsule None
author | bgruening |
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date | Sun, 08 Feb 2015 10:05:20 -0500 |
parents | |
children | 5a0d0bee4f8d |
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1 <tool id="diamond_database_builder" name="Diamond" tool_type="manage_data" version="0.0.1"> | |
2 <description> Database builder</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.6.13">diamond</requirement> | |
5 </requirements> | |
6 <command interpreter="python"> | |
7 data_manager_diamond_database_builder.py "${out_file}" | |
8 </command> | |
9 <inputs> | |
10 <param type="text" name="database_name" value="" label="Database name or description" | |
11 help="This will be shown to the user in the database selectbox."/> | |
12 <param type="text" name="database_id" value="" label="Database ID" help="This needs to be unique. No whitespaces allowed. Use underscores." /> | |
13 <conditional name="reference_source"> | |
14 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | |
15 <option value="ncbi">NCBI</option> | |
16 <option value="url">URL</option> | |
17 <option value="history" selected="True" help="Recommended to archive the original FASTA file as well.">History</option> | |
18 <option value="directory">Directory on Server</option> | |
19 </param> | |
20 <when value="ncbi"> | |
21 <param type="text" name="requested_identifier" value="" label="NCBI identifier" help="e.g. nr" optional="False" /> | |
22 </when> | |
23 <when value="url"> | |
24 <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" /> | |
25 </when> | |
26 <when value="history"> | |
27 <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" /> | |
28 </when> | |
29 <when value="directory"> | |
30 <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" /> | |
31 <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to orignal data instead of copying" checked="False" /> | |
32 </when> | |
33 </conditional> | |
34 </inputs> | |
35 <outputs> | |
36 <data name="out_file" format="data_manager_json"/> | |
37 </outputs> | |
38 <help> | |
39 | |
40 .. class:: infomark | |
41 | |
42 NCBI databases can be downded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/ | |
43 For example the NR database can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz | |
44 | |
45 </help> | |
46 </tool> |