Mercurial > repos > taoufik > microarrays

comparison query_microarray_datasets/Get_Datasets.xml @ 1:842f8effaf59 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Deleted selected files
author taoufik
date Thu, 27 Dec 2018 06:56:28 -0500
parents cf862e6a6ddb
children
comparison
equal deleted inserted replaced
0:cf862e6a6ddb 1:842f8effaf59
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>