Mercurial > repos > biocomp-ibens > data_manager_build_alfa_indexes
comparison data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.xml @ 0:f68a60c3d768 draft default tip
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author | biocomp-ibens |
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date | Wed, 16 May 2018 09:56:43 -0400 |
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1 <tool id="build_alfa_indexes" name="ALFA indexes" version="0.0.1" tool_type="manage_data"> | |
2 <description>build ALFA indexes from automatically downloaded gtf annotation file</description> | |
3 <!-- ALFA requires bedtools suite v2.20.0 and above --> | |
4 <requirements> | |
5 <requirement type="package" version="2.24">bedtools</requirement> | |
6 <requirement type="package" version="1.2">samtools</requirement> | |
7 <requirement type="package" version="1.4">matplotlib</requirement> | |
8 </requirements> | |
9 | |
10 <command interpreter="python">data_manager_build_alfa_indexes.py -e "${reference_source['kingdom']}" "${reference_source['species_name']}" -o "${out_file}" "$__tool_directory__"</command> | |
11 | |
12 <inputs> | |
13 <conditional name="reference_source"> | |
14 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | |
15 <option value="ensembl" selected="True">Ensembl Genomes Websites</option> | |
16 </param> | |
17 <when value="ensembl"> | |
18 <param name="kingdom" type="select" label="Select the ensembl website where to fetch the genome"> | |
19 <option value="vertebrates" selected="True">Ensembl (Vertebrates)</option> | |
20 <option value="bacteria" selected="True">Ensembl Bacteria</option> | |
21 <option value="fungi" selected="True">Ensembl Fungi</option> | |
22 <option value="metazoa" selected="True">Ensembl Metazoa</option> | |
23 <option value="plants" selected="True">Ensembl Plants</option> | |
24 <option value="protists" selected="True">Ensembl Protists</option> | |
25 </param> | |
26 <param name="species_name" type="text" value="Homo sapiens" label="Complete Species_Name" optional="False"> | |
27 <validator type="empty_field" message="Please, enter a species name."/> | |
28 </param> | |
29 </when> | |
30 </conditional> | |
31 </inputs> | |
32 | |
33 <outputs> | |
34 <data name="out_file" format="data_manager_json"/> | |
35 </outputs> | |
36 | |
37 <help> | |
38 <![CDATA[ | |
39 **What it does** | |
40 | |
41 | |
42 | 1. The tool asks the admin to enter a *species_name* and automatically download the last release of the corresponding gtf annotation file on Ensembl. | |
43 | | |
44 | 2. The tool calls ALFA.py to generate the alfa indexes from this gtf file. | |
45 | | |
46 | 3. Resulting indexes are stored in the child directory *alfa_indexes/* of the dir *<galaxy_data_manager_data_path>* defined in *config/galaxy.ini* | |
47 | | |
48 | 4. Finally, the tool adds the new entry to the table *alfa_indexes.loc*. This .loc file is where the data table *alfa_indexes* points, as defined in *config/shed_tool_data_table.conf.xml* | |
49 | | |
50 | 5. At the end of the process, when a user will use `alfa`_ , the built-in indexes corresponding to the *species_name* will be available | |
51 | |
52 .. _alfa: https://toolshed.g2.bx.psu.edu/view/charles-bernard/alfa | |
53 | |
54 ]]> | |
55 </help> | |
56 | |
57 </tool> |