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comparison ImportDataFromMatrix.xml @ 6:3ce32282f6a4 draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 228bd64b01f184d5d8ebc9f65fe0add2d45ed4fe
author sblanck
date Tue, 26 Jun 2018 08:54:45 -0400
parents 1024245abc70
children
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equal deleted inserted replaced
5:ca46ad51fe5a 6:3ce32282f6a4
2 2
3 <description>Quality control and normalization of a custom matrix expression data</description> 3 <description>Quality control and normalization of a custom matrix expression data</description>
4 4
5 <requirements> 5 <requirements>
6 <requirement type="package">bioconductor-biobase</requirement> 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> 7 <requirement type="package">bioconductor-limma</requirement>
10 <requirement type="package">bioconductor-biobase</requirement>
11 <requirement type="package">bioconductor-affy</requirement> 8 <requirement type="package">bioconductor-affy</requirement>
12 <requirement type="package">bioconductor-affyplm</requirement> 9 <requirement type="package">bioconductor-affyplm</requirement>
13 <requirement type="package">r-jsonlite</requirement> 10 <requirement type="package">r-jsonlite</requirement>
14 <requirement type="package">r-dplyr</requirement> 11 <requirement type="package">r-dplyr</requirement>
15 <requirement type="package">r-optparse</requirement> 12 <requirement type="package">r-optparse</requirement>
24 <![CDATA[ 21 <![CDATA[
25 Rscript --vanilla 22 Rscript --vanilla
26 ${__tool_directory__}/ImportDataFromMatrix.R 23 ${__tool_directory__}/ImportDataFromMatrix.R
27 --input $input 24 --input $input
28 --normalization $normalization 25 --normalization $normalization
29 --conditions $conditions
30 --annotations $annotations 26 --annotations $annotations
31 --rdataoutput $result_export_eset 27 --rdataoutput $result_export_eset
32 --htmloutput $result_html 28 --htmloutput $result_html
33 --htmloutputpath $result_html.files_path 29 --htmloutputpath $result_html.files_path
34 --htmltemplate ${__tool_directory__}/ImportDataFromMatrix_tpl.html 30 --htmltemplate ${__tool_directory__}/ImportDataFromMatrix_tpl.html
40 <param name="normalization" type="select" label="Preprocessing/normalization"> 36 <param name="normalization" type="select" label="Preprocessing/normalization">
41 <option value="quantile">quantile normalization + log2</option> 37 <option value="quantile">quantile normalization + log2</option>
42 <option value="log2">log2 only</option> 38 <option value="log2">log2 only</option>
43 <option value="none">none</option> 39 <option value="none">none</option>
44 </param> 40 </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"/> 41 <param name="annotations" type="text" label="Annotation GPL code" help="GPL code for annotations"/>
47 </inputs> 42 </inputs>
48 43
49 <outputs> 44 <outputs>
50 <data format="rdata" name="result_export_eset" label="export normalized expressionSet"/> 45 <data format="rdata" name="result_export_eset" label="export normalized expressionSet"/>