smagexp: AffyQCnormalization.xml annotate

annotate AffyQCnormalization.xml @ 15:c05f899d5dcd draft

planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160-dirty

author	sblanck
date	Tue, 16 May 2017 02:08:10 -0400
parents	328f4031e5d3
children	161fe6ba75d7

rev	line source
15 c05f899d5dcd planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160-dirty sblanck parents: 9 diff changeset	1 <tool id="QCnormalization" name="QCnormalization" version="1.0.0">
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	2
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	3 <description>Quality control and normalization of affymetrix expression data</description>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	4
8 7f74250a083d planemo upload sblanck parents: 2 diff changeset	5 <requirements>
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	6 <requirement type="package" version="0.1.0">r-smagexp</requirement>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	7 </requirements>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	8
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	9 <stdio>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	10 <exit_code range="1:" />
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	11 <regex match="Warning" source="both" level="warning"/>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	12 </stdio>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	13
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	14 <command>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	15 <![CDATA[
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	16 Rscript
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	17 ${__tool_directory__}/AffyQCnormalization.R
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	18 --input "#for $input in $inputs# $input;$input.name, #end for#"
8 7f74250a083d planemo upload sblanck parents: 2 diff changeset	19 --normalization ${normalization}
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	20 --rdataoutput $result_export_eset
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	21 --htmloutput $result_html
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	22 --htmloutputpath $result_html.files_path
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	23 --htmltemplate ${__tool_directory__}/AffyQCnormalization_tpl.html
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	24 ]]>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	25 </command>
2 93451f832736 Uploaded sblanck parents: diff changeset	26
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	27 <inputs>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	28 <param name="inputs" type="data" format="cel" multiple="true" label=".CEL files" help=".CEL files to be used"/>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	29 <param name="normalization" type="select" label="Preprocessing/normalization">
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	30 <option value="rma">rma (backgroung correction + quantile normalization + log2)</option>
2 93451f832736 Uploaded sblanck parents: diff changeset	31 <option value="quantile">quantile normalization + log2</option>
93451f832736 Uploaded sblanck parents: diff changeset	32 <option value="background">background correction + log2</option>
93451f832736 Uploaded sblanck parents: diff changeset	33 <option value="log2">log2 only</option>
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	34 </param>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	35 </inputs>
2 93451f832736 Uploaded sblanck parents: diff changeset	36
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	37 <outputs>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	38 <data format="rdata" name="result_export_eset" label="export normalized expressionSet"/>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	39 <data format="html" name="result_html" label="QC result"/>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	40 </outputs>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	41
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	42 <help>
2 93451f832736 Uploaded sblanck parents: diff changeset	43 <![CDATA[
93451f832736 Uploaded sblanck parents: diff changeset	44 What it does
93451f832736 Uploaded sblanck parents: diff changeset	45
93451f832736 Uploaded sblanck parents: diff changeset	46 The QCnormalization tool offers to ensure the quality of the data and to normalize them. Several normalization methods are available :
93451f832736 Uploaded sblanck parents: diff changeset	47
93451f832736 Uploaded sblanck parents: diff changeset	48 * rma normalization
93451f832736 Uploaded sblanck parents: diff changeset	49 * quantile normalization + log2
93451f832736 Uploaded sblanck parents: diff changeset	50 * background correction + log2
93451f832736 Uploaded sblanck parents: diff changeset	51 * log2 only
93451f832736 Uploaded sblanck parents: diff changeset	52
93451f832736 Uploaded sblanck parents: diff changeset	53 Results
93451f832736 Uploaded sblanck parents: diff changeset	54
93451f832736 Uploaded sblanck parents: diff changeset	55 - Several quality figures : microarray images, boxplots and MA plots
93451f832736 Uploaded sblanck parents: diff changeset	56 - Rdata object containing the normalized data for further analysis
93451f832736 Uploaded sblanck parents: diff changeset	57
93451f832736 Uploaded sblanck parents: diff changeset	58 ]]>
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	59 </help>
2 93451f832736 Uploaded sblanck parents: diff changeset	60
93451f832736 Uploaded sblanck parents: diff changeset	61 </tool>

Mercurial > repos > sblanck > smagexp

annotate AffyQCnormalization.xml @ 15:c05f899d5dcd draft