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comparison data_manager/data_manager_ceas_fetch_annotations.xml @ 4:4e2883bb058d draft

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Synchronise version with one on main toolshed (version of 30/06/2015)
author pjbriggs
date Wed, 10 Aug 2016 11:04:42 -0400
parents d9032bb158b9
children b5d686bb9d6f
comparison
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3:82df5af2995f 4:4e2883bb058d
1 <tool id="data_manager_fetch_ceas_annotations" name="Fetch CEAS annotation" version="0.0.1" tool_type="manage_data"> 1 <tool id="data_manager_fetch_ceas_annotations" name="Fetch CEAS annotation" version="0.0.1" tool_type="manage_data">
2 <requirements>
3 <requirement type="package" version="1.2.5">python_mysqldb</requirement>
4 <requirement type="package" version="0.7.1">bx_python</requirement>
5 <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement>
6 </requirements>
2 <description>Fetch and install annotation databases for CEAS</description> 7 <description>Fetch and install annotation databases for CEAS</description>
3 <command interpreter="python">data_manager_ceas_fetch_annotations.py 8 <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 "${out_file}" 9 "${out_file}"
8 "${description}"</command> 10 "${description}"</command>
9 <inputs> 11 <inputs>
10 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> 12 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
11 <param type="text" name="description" value="" label="Description of annotation" /> 13 <param type="text" name="unique_id" label="Internal identifier"
14 help="Identifier string to associate with the annotation e.g. 'mm9_generic'" />
15 <param type="text" name="description" value="" size="50"
16 label="Description of annotation"
17 help="Text that will be displayed to the user when selecting which annotation to use" />
12 <conditional name="reference_source"> 18 <conditional name="reference_source">
13 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> 19 <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> 20 <option value="web" selected="True">CEAS website</option>
15 <!-- Not implemented for now 21 <option value="server">File on the server</option>
16 <option value="history">History</option> 22 <option value="from_wig">Generated from wig file</option>
17 -->
18 <option value="directory">Directory on Server</option>
19 </param> 23 </param>
20 <when value="ceas_web"> 24 <when value="web">
21 <param type="select" name="annotation_url"> 25 <param type="select" name="annotation_url">
22 <option value="http://liulab.dfci.harvard.edu/CEAS/src/hg18.refGene.gz">hg18</option> 26 <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> 27 <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> 28 <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> 29 <option value="http://liulab.dfci.harvard.edu/CEAS/src/mm9.refGene.gz">mm9</option>
27 <option value="http://liulab.dfci.harvard.edu/CEAS/src/dm3.refGene.gz">dm3</option> 31 <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> 32 <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> 33 <option value="http://liulab.dfci.harvard.edu/CEAS/src/ce6.refGene.gz">ce6</option>
30 </param> 34 </param>
31 </when> 35 </when>
32 <!-- Not implemented for now 36 <when value="server">
33 <when value="history"> 37 <param type="text" name="annotation_filename" value="" size="50"
34 <param name="input_annotation" type="data" format="fasta" label="Annotation File" multiple="False" optional="False" /> 38 label="Full path to CEAS annotation table file on disk" 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" /> 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> 40 </when>
41 <when value="from_wig">
42 <param type="data" format="wig" name="wig_file" value=""
43 label="Wig file to use for the background genome annotation"
44 help="Will be used as input to build_genomeBG" />
45 <param type="select" name="gene_annotation"
46 label="Gene annotation from UCSC">
47 <option value="refGene">refGene</option>
48 </param>
49 </when>
41 </conditional> 50 </conditional>
42 </inputs> 51 </inputs>
43 <outputs> 52 <outputs>
44 <data name="out_file" format="data_manager_json"/> 53 <data name="out_file" format="data_manager_json"/>
45 </outputs> 54 </outputs>
46 <tests> 55 <tests>
47 <test> 56 <test>
48 <param name="dbkey" value="anoGam1"/> 57 <!-- No tests defined, yet -->
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> 58 </test>
57 </tests> 59 </tests>
58 <help> 60 <help>
61
62 .. class:: infomark
63
59 **What it does** 64 **What it does**
60 65
61 Fetches an annotation database from the CEAS website, Galaxy history, or a server directory 66 Adds a CEAS gene annotation table file to the *ceas_annotations"* data table. The
62 and populates the "ceas_annotations" data table. 67 database file can be downloaded from the CEAS website, imported from a file on the
68 Galaxy server, or generated from a ``wig`` file in a Galaxy history.
69
70 **Notice:** If you leave the identifier or description blank then they will be
71 generated automatically.
63 72
64 ------ 73 ------
65 74
66
67
68 .. class:: infomark 75 .. class:: infomark
69 76
70 **Notice:** If you leave name, description, or id blank, it will be generated automatically. 77 **Fetching, uploading or creating gene annotation table files**
71 78
79 The gene annotation table files are SQLite database files which are on the CEAS website:
80
81 - http://liulab.dfci.harvard.edu/CEAS/usermanual.html
82
83 The data manager allows you to fetch a pre-built table from the CEAS website; note
84 that these are based on the ``RefSeq`` annotation and are only available for a subset
85 of genome builds.
86
87 To create an annotation table for a different genome build or a different annotation,
88 use the *Generated from wig* file option. This runs the CEAS utility ``build_genomeBG``
89 to make a custom table from a wig file, which represents the genome background (e.g.
90 a wig file created from the ``control lambda`` bedgraph file output from MACS2).
91
92 Alternatively if you already have an existing custom annotation file then this can be
93 imported from a path on the Galaxy server.
72 </help> 94 </help>
73 </tool> 95 </tool>