Mercurial > repos > ppericard > mixomics_blocksplsda

annotate matCor_addVar.xml @ 5:1ee8d2c20c0a draft

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
author ppericard
date Tue, 10 Mar 2020 06:27:02 -0400
parents b0ab97ffc2a1
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1 <tool id="matCor_addVar" name="matCor_addVar" version="0.3.0" profile="16.04" workflow_compatible="true">
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3 <description>computes all the correlations needed to plot a correlation circle and determines which correlation circles can be superimposed</description>
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5 <requirements>
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6 <requirement type="package" version="6.8">bioconductor-mixomics</requirement>
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7 <requirement type="package" version="2.0">r-argparse</requirement>
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8 </requirements>
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10 <stdio>
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11 <!-- <exit_code range="1:" level="fatal" /> -->
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12 </stdio>
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14 <command detect_errors="aggressive">
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15 <![CDATA[
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16 Rscript
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17 ${__tool_directory__}/matCor_addVar_wrapper.R
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18 --input_rdata ${input_rdata}
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19 --cutoff_comp ${cutoff_comp}
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20 --mat_block_Y_file ${mat_block_Y}
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21 --output_rdata ${output_rdata}
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22 --output_blocks_comb ${output_blocks_comb}
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23 ]]>
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24 </command>
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26 <inputs>
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27 <param name="input_rdata" type="data" format="rdata"
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28 label="Input RData file from block.SPLSDA"
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29 help="This is the RData output file from the block.splsda function." />
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30 <param name="cutoff_comp" type="float" value="0.8" min="0" max="1"
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31 label="Cutoff comp"
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32 help="[cutoff_comp] Two correlation circles will be superimposed if the correlation of their first and second axis is greater than cutoff_comp in absolute value." />
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33 <param name="mat_block_Y" type="data" format="tabular"
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34 label="Matrix Block Y"
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35 help="Matrix Block Y in tabular format. This table contains the name of the samples in the first column. The other columns correspond to phenotypes. For each of these other columns, a column determines which sample is associated with this phenotype (value equals to 1) or not (value equals to 0). The name of the samples in Matrix Block Y (transposed), in the sample metadata (transposed) and for all datasets have to be in the same order" />
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36 </inputs>
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38 <outputs>
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39 <data name="output_rdata" format="rdata" label="${tool.name}_output.rdata" />
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40 <data name="output_blocks_comb" format="tabular" label="${tool.name}_blocks_comb.tsv" />
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41 </outputs>
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43 <tests>
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44 </tests>
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46 <help>
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47 </help>
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49 </tool>