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comparison multivariate_config.xml @ 4:5526f8258e8a draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 0f382a5296aae9bfc77df06b0a5ad493eb3c01f3
author ethevenot
date Wed, 28 Feb 2018 09:59:25 -0500
parents e91de3b04320
children
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3:e91de3b04320 4:5526f8258e8a
1 <tool id="Multivariate" name="Multivariate" version="2.3.8"> 1 <tool id="Multivariate" name="Multivariate" version="2.3.10">
2 <description>PCA, PLS and OPLS</description> 2 <description>PCA, PLS and OPLS</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.3.1">R</requirement> 5 <requirement type="package" version="1.1_4">r-batch</requirement>
6 <requirement type="package">r-batch</requirement> 6 <requirement type="package" version="1.10.0">bioconductor-ropls</requirement>
7 <requirement type="package">bioconductor-ropls</requirement>
8 </requirements> 7 </requirements>
9 8
10 <stdio> 9 <stdio>
11 <exit_code range="1:" level="fatal" /> 10 <exit_code range="1:" level="fatal" />
12 </stdio> 11 </stdio>
43 42
44 sampleMetadata_out "$sampleMetadata_out" 43 sampleMetadata_out "$sampleMetadata_out"
45 variableMetadata_out "$variableMetadata_out" 44 variableMetadata_out "$variableMetadata_out"
46 figure "$figure" 45 figure "$figure"
47 information "$information" 46 information "$information"
47
48 #if $save_rdata:
49 ropls_out "$ropls_out"
50 #end if
48 ]]></command> 51 ]]></command>
49 52
50 <inputs> 53 <inputs>
51 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" /> 54 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" />
52 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" /> 55 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" />
179 <option value="10">10</option> 182 <option value="10">10</option>
180 </param> 183 </param>
181 184
182 </when> 185 </when>
183 </conditional> 186 </conditional>
184 187 <param name="save_rdata" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save RData in your history"
188 help="Save the R ropls::opls object in your history for ad hoc analysis and graphing (outside Galaxy, this requires package 'bioconductor-ropls')"/>
185 </inputs> 189 </inputs>
186 190
187 <outputs> 191 <outputs>
188 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data> 192 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
189 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data> 193 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
190 <data name="figure" label="${tool.name}__figure.pdf" format="pdf"/> 194 <data name="figure" label="${tool.name}_figure.pdf" format="pdf"/>
191 <data name="information" label="${tool.name}__information.txt" format="txt"/> 195 <data name="information" label="${tool.name}_information.txt" format="txt"/>
196 <!-- how would an ropls.rdata datatype be added if that were the desired choice here instead? Specifically, could it be created as part of tool installation? -->
197 <data name="ropls_out" label="${tool.name}_${dataMatrix_in.name}.RData" format="rdata">
198 <filter>save_rdata</filter>
199 </data>
192 </outputs> 200 </outputs>
193 201
194 <tests> 202 <tests>
195 <test> 203 <test>
196 <param name="dataMatrix_in" value="input-dataMatrix.tsv"/> 204 <param name="dataMatrix_in" value="input-dataMatrix.tsv"/>