Mercurial > repos > taoufik > dream_challenge
comparison Format_Dream.xml @ 0:4eb60f0a4fdb draft
Uploaded
author | taoufik |
---|---|
date | Sat, 26 Jan 2019 19:01:54 -0500 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:4eb60f0a4fdb |
---|---|
1 <tool id="Format_Dream" name="Dream Tabular" version="20181019" hidden="false"> | |
2 <description> Read DataSet into Rdata Binary for the Preprocessing Step. </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="1.11.4" owner="defaults">r-data.table</requirement> | |
7 </requirements> | |
8 <command> | |
9 <![CDATA[ | |
10 Rscript '$__tool_directory__/FormatDream.R' | |
11 datasetsource $inputdata | |
12 ]]> | |
13 | |
14 </command> | |
15 <inputs> | |
16 <param name="inputdata" type="data" format="tabular" label="Select File."/> | |
17 | |
18 </inputs> | |
19 <outputs> | |
20 <data name="Format_Dream.tsv" format="tabular" from_work_dir="Format_Dream.tsv" label="Format_Dream.tsv"> | |
21 </data> | |
22 </outputs> | |
23 <stdio> | |
24 <exit_code range="1:" level="fatal" /> | |
25 </stdio> | |
26 <help> | |
27 | |
28 .. class:: infomark | |
29 | |
30 **Authors** Bensellak Taoufik bensellak@ensat.ac.ma, El Messaoudi Idrissi Mohcine mohcine.elmessaoudi@gmail.com, Ahmed Moussa ahmed.moussa2@gmail.com . | |
31 | |
32 --------------------------------------------------- | |
33 | |
34 ================================== | |
35 Read Microarray DataSet | |
36 ================================== | |
37 | |
38 ----------- | |
39 Description | |
40 ----------- | |
41 | |
42 This tool is used for reading choosen dataset in order to process, dataset could be imported or selected from available datasets. | |
43 | |
44 ----------------- | |
45 Workflow position | |
46 ----------------- | |
47 | |
48 **Upstream tools** | |
49 | |
50 +------------------------+--------------------------------------------------+--------+ | |
51 | Name | output file |format | | |
52 +========================+==================================================+========+ | |
53 | Get List Datasets | Projects.Informations.on.technology.RData | Rdata | | |
54 +------------------------+--------------------------------------------------+--------+ | |
55 | Get List Datasets | Get.List.DataSets.Microarrays.on.technology.tsv | Tabular| | |
56 +------------------------+--------------------------------------------------+--------+ | |
57 | Make Design | Imported.Project.Informations.RData | Rdata | | |
58 +------------------------+--------------------------------------------------+--------+ | |
59 | |
60 | |
61 **Downstream tools** | |
62 | |
63 +-------------------------------------------+----------------------------------+----------+ | |
64 | Name | Output file | Format | | |
65 +===========================================+==================================+==========+ | |
66 |Preprocess.DataSet.Microarray | Preprocess.Project.Data.RData | RData | | |
67 +-------------------------------------------+----------------------------------+----------+ | |
68 |Matrix.Data | Matrix.Data.tsv | Tabular | | |
69 +-------------------------------------------+----------------------------------+----------+ | |
70 | |
71 ----------- | |
72 Input files | |
73 ----------- | |
74 | |
75 +---------------------------------+------------+ | |
76 | Parameter : num + label | Format | | |
77 +=================================+============+ | |
78 | image (both intern and exterm ) | Rdata | | |
79 +---------------------------------+------------+ | |
80 | datasetsnames (only intern) | Tabular | | |
81 +---------------------------------+------------+ | |
82 | |
83 ------------ | |
84 Output files | |
85 ------------ | |
86 | |
87 **MicroArrayObject.RData** Both for intern and extern datasets | |
88 | |
89 **design.tsv** Only for extern datasets | |
90 | |
91 ------------------------------ | |
92 General schema of the workflow | |
93 ------------------------------ | |
94 | |
95 .. image:: ./images/workflow.jpg | |
96 :height: 800 | |
97 :width: 700 | |
98 | |
99 </help> | |
100 </tool> |