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comparison query_microarray_datasets/Get_Datasets.xml @ 0:cf862e6a6ddb draft

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author taoufik
date Thu, 27 Dec 2018 05:54:24 -0500
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1 <tool id="Get_Datasets" name="Query GEO Database" version="20181028">
2 <description> Query Gene Expression Omnibus (GEO) Database using accession code. </description>
3 <requirements>
4 <requirement type="package" version="3.4.1_0">r-base</requirement>
5 <requirement type="package" version="1.1_4">r-batch</requirement>
6 <requirement type="package" version="2.42.0">bioconductor-geoquery</requirement>
7 </requirements>
8 <command>
9 <![CDATA[
10 Rscript '$__tool_directory__/GetDatasets.R' GeoCode $GeoCode
11 ]]>
12 </command>
13 <inputs>
14 <param name="GeoCode" size="40" type="text" value="GSE50628" label="GEO accession" help="Gene Expression Omnibus (GEO) accession code">
15 <sanitizer>
16 <valid initial="string.printable,string.digits">
17 </valid>
18 </sanitizer>
19 </param>
20 </inputs>
21 <outputs>
22 <data format="microarray" type="microarray" name="Geo Raw">
23 <discover_datasets pattern="(?P&lt;name&gt;.*)" ext="microarray" format="microarray" type="microarray" visible="true" assign_primary_output="true" directory="CEL" />
24 </data>
25 </outputs>
26 <stdio>
27 <exit_code range="1:" level="fatal" />
28 </stdio>
29 <help>
30
31 .. class:: infomark
32
33 **Authors** Bensellak Taoufik bensellak.taoufik@gmail.com, El Messaoudi Idrissi Mohcine mohcine.elmessaoudi@gmail.com , Ahmed Moussa ahmed.moussa2@gmail.com .
34
35 ---------------------------------------------------
36
37 ==================================================================
38 Query Gene Expression Omnibus (GEO) Database.
39 ==================================================================
40
41 -----------
42 Description
43 -----------
44
45 This tool is used for querying Gene Expression Omnibus Database.
46
47 **GEO accession**
48
49 GEO Accession code
50
51 -----------------
52 Workflow position
53 -----------------
54
55 **Upstream tools**
56
57 +------------------------+------------------+--------+-----------+
58 | Name | output file |format | parameter |
59 +========================+==================+========+===========+
60 | NA | NA | NA | NA |
61 +------------------------+------------------+--------+-----------+
62
63
64 **Downstream tools**
65
66 +-----------------------------------------------+------------------------------------------------+------------+
67 | Name | Output file | Format |
68 +===============================================+================================================+============+
69 | Create Desig | DataSet.Design.tsv,DataSet.Informations.RData | tsv,RData |
70 +-----------------------------------------------+------------------------------------------------+------------+
71
72 -----------
73 Input files
74 -----------
75
76 +---------------------------+------------+
77 | Parameter : num + label | Format |
78 +===========================+============+
79 | GEO accession | String |
80 +---------------------------+------------+
81
82 ------------
83 Output files
84 ------------
85
86 **Set of raw samples**
87
88 ------------------------------
89 General schema of the workflow
90 ------------------------------
91
92 .. image:: ./workflow.jpg
93 :height: 800
94 :width: 700
95
96 </help>
97 </tool>