Mercurial > repos > sblanck > smagexp

comparison ImportDataFromMatrix.xml @ 0:1024245abc70 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
author sblanck
date Thu, 22 Feb 2018 08:38:22 -0500
parents
children 3ce32282f6a4
comparison
equal deleted inserted replaced
-1:000000000000 0:1024245abc70
1 <tool id="importMatrixData" name="Import custom data" version="1.0.0">
2
3 <description>Quality control and normalization of a custom matrix expression data</description>
4
5 <requirements>
6 <requirement type="package">bioconductor-biobase</requirement>
7 <requirement type="package">bioconductor-geoquery</requirement>
8 <requirement type="package">bioconductor-geometadb</requirement>
9 <requirement type="package">bioconductor-limma</requirement>
10 <requirement type="package">bioconductor-biobase</requirement>
11 <requirement type="package">bioconductor-affy</requirement>
12 <requirement type="package">bioconductor-affyplm</requirement>
13 <requirement type="package">r-jsonlite</requirement>
14 <requirement type="package">r-dplyr</requirement>
15 <requirement type="package">r-optparse</requirement>
16 </requirements>
17
18 <stdio>
19 <exit_code range="1:" />
20 <regex match="Warning" source="both" level="warning"/>
21 </stdio>
22
23 <command>
24 <![CDATA[
25 Rscript --vanilla
26 ${__tool_directory__}/ImportDataFromMatrix.R
27 --input $input
28 --normalization $normalization
29 --conditions $conditions
30 --annotations $annotations
31 --rdataoutput $result_export_eset
32 --htmloutput $result_html
33 --htmloutputpath $result_html.files_path
34 --htmltemplate ${__tool_directory__}/ImportDataFromMatrix_tpl.html
35 ]]>
36 </command>
37
38 <inputs>
39 <param name="input" type="data" format="tabular" label="Input data" help="Input data"/>
40 <param name="normalization" type="select" label="Preprocessing/normalization">
41 <option value="quantile">quantile normalization + log2</option>
42 <option value="log2">log2 only</option>
43 <option value="none">none</option>
44 </param>
45 <param name="conditions" type="data" format="cond" label="Conditions" help="conditions associated with the input file"/>
46 <param name="annotations" type="text" label="Annotation GPL code" help="GPL code for annotations"/>
47 </inputs>
48
49 <outputs>
50 <data format="rdata" name="result_export_eset" label="export normalized expressionSet"/>
51 <data format="html" name="result_html" label="QC result"/>
52 </outputs>
53
54 <help>
55 <![CDATA[
56 **What it does**
57
58 This tool imports data stored in a tabular text file.
59 Column titles (chip IDs) must match the IDs of the .cond file.
60 GPL annotation code is also required to fetch annotations from GEO.
61
62 **Exemple**
63
64 Header of input tabular text file
65 ::
66
67
68 "" "GSM80460" "GSM80461" "GSM80462" "GSM80463" "GSM80464"
69 "1007_s_at" -0.0513991525066443 0.306845500314283 0.0854246562526777 -0.142417044615852 0.0854246562526777
70 "1053_at" -0.187707155126729 -0.488026018218199 -0.282789700980404 0.160920188181103 0.989865622866287
71 "117_at" 0.814755482809874 -2.15842936260448 -0.125006361067033 -0.256700472111743 0.0114956388378294
72 "121_at" -0.0558912008920451 -0.0649174766813385 0.49467161164755 -0.0892673380970874 0.113700499164728
73 "1294_at" 0.961993677420255 -0.0320936297098533 -0.169744675832317 -0.0969617298870879 -0.181149439104566
74 "1316_at" 0.0454429707611671 0.43616183931445 -0.766111939825723 -0.182786075741673 0.599317793698226
75 "1405_i_at" 2.23450132056221 0.369606070031838 -1.06190243892591 -0.190997225060914 0.595503660502742
76
77
78 The .cond file should look like this
79 ::
80
81 GSM80460 series of 16 tumors GSM80460 OSCE-2T SERIES OF 16 TUMORS
82 GSM80461 series of 16 tumors GSM80461 OSCE-4T Series of 16 Tumors
83 GSM80462 series of 16 tumors GSM80462 OSCE-6T Series of 16 Tumors
84 GSM80476 series of 4 normals GSM80476 OSCE-2N Series of 4 Normals
85 GSM80477 series of 4 normals GSM80477 OSCE-9N Series of 4 Normals
86
87
88 **Results**
89 - Boxplots and MA plots
90 - Rdata object containing the data for further analysis.
91 ]]>
92 </help>
93
94 </tool>