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comparison data_manager/data_manager_ceas_fetch_annotations.xml @ 1:d9032bb158b9 draft

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Add in data manager for CEAS annotation databases.
author pjbriggs
date Wed, 28 Jan 2015 05:04:46 -0500
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children 4e2883bb058d
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0:8b25779ee261 1:d9032bb158b9
1 <tool id="data_manager_fetch_ceas_annotations" name="Fetch CEAS annotation" version="0.0.1" tool_type="manage_data">
2 <description>Fetch and install annotation databases for CEAS</description>
3 <command interpreter="python">data_manager_ceas_fetch_annotations.py
4 #if str( $reference_source.reference_source_selector ) == "ceas_web"
5 --download=$reference_source.annotation_url
6 #end if
7 "${out_file}"
8 "${description}"</command>
9 <inputs>
10 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
11 <param type="text" name="description" value="" label="Description of annotation" />
12 <conditional name="reference_source">
13 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
14 <option value="ceas_web" selected="True">CEAS website</option>
15 <!-- Not implemented for now
16 <option value="history">History</option>
17 -->
18 <option value="directory">Directory on Server</option>
19 </param>
20 <when value="ceas_web">
21 <param type="select" name="annotation_url">
22 <option value="http://liulab.dfci.harvard.edu/CEAS/src/hg18.refGene.gz">hg18</option>
23 <option value="http://liulab.dfci.harvard.edu/CEAS/src/hg19.refGene.gz">hg19</option>
24 <option value="http://liulab.dfci.harvard.edu/CEAS/src/mm8.refGene.gz">mm8</option>
25 <option value="http://liulab.dfci.harvard.edu/CEAS/src/mm9.refGene.gz">mm9</option>
26 <option value="http://liulab.dfci.harvard.edu/CEAS/src/dm2.refGene.gz">dm2</option>
27 <option value="http://liulab.dfci.harvard.edu/CEAS/src/dm3.refGene.gz">dm3</option>
28 <option value="http://liulab.dfci.harvard.edu/CEAS/src/ce4.refGene.gz">ce4</option>
29 <option value="http://liulab.dfci.harvard.edu/CEAS/src/ce6.refGene.gz">ce6</option>
30 </param>
31 </when>
32 <!-- Not implemented for now
33 <when value="history">
34 <param name="input_annotation" type="data" format="fasta" label="Annotation File" multiple="False" optional="False" />
35 </when>
36 -->
37 <when value="directory">
38 <param type="text" name="annotation_filename" value="" label="Full path to CEAS annotation table file on disk" optional="False" />
39 <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to orignal data instead of copying" checked="False" />
40 </when>
41 </conditional>
42 </inputs>
43 <outputs>
44 <data name="out_file" format="data_manager_json"/>
45 </outputs>
46 <tests>
47 <test>
48 <param name="dbkey" value="anoGam1"/>
49 <param name="sequence_name" value=""/>
50 <param name="sequence_desc" value=""/>
51 <param name="sequence_id" value=""/>
52 <param name="reference_source_selector" value="history"/>
53 <param name="input_fasta" value="phiX174.fasta"/>
54 <param name="sort_selector" value="as_is"/>
55 <output name="out_file" file="phiX174_as_anoGam1.data_manager_json"/>
56 </test>
57 </tests>
58 <help>
59 **What it does**
60
61 Fetches an annotation database from the CEAS website, Galaxy history, or a server directory
62 and populates the "ceas_annotations" data table.
63
64 ------
65
66
67
68 .. class:: infomark
69
70 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
71
72 </help>
73 </tool>