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annotate matCorAddVar.xml @ 1:e93350dc99f1 draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 1eda261d4fe137d6e8806b0c6af7eaf12d11ac95"
author ppericard
date Thu, 15 Oct 2020 12:22:25 +0000
parents d0b77b926863
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1 <tool id="matCorAddVar" name="matCorAddVar" version="0.6+galaxy0" profile="16.04" workflow_compatible="true">
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3 <description>determine the correlation circles that can be overlaid and compute the correlations</description>
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5 <requirements>
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6 <requirement type="package" version="0.6">r-viscorvar</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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13
0
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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__}/matCorAddVar_wrapper.R
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18 --input_rdata ${input_rdata}
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19 ##--cutoff_comp ${cutoff_comp}
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20 --cutoff_comp 0.75
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21 #if str($var_of_interest_file) !='':
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22 --interest_var_file ${var_of_interest_file}
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23 #end if
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24 --block_Y_file ${block_Y}
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25 --output_rdata ${output_rdata}
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26 --output_response_var ${output_response_var}
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27 --output_blocks_comb ${output_blocks_comb}
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28 ]]>
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29 </command>
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30
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31 <inputs>
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32 <param name="input_rdata" type="data" format="rdata"
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33 label="Input RData file from block.SPLSDA"
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34 help="This is the RData output file from the block.splsda function." />
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35 <param name="block_Y" type="data" format="tabular"
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36 label="Block Y"
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37 help="[block_Y] (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 Block Y (transposed), in the sample metadata (transposed) and for all datasets have to be in the same order" />
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38 <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
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39 <param name="var_of_interest_file" type="data" format="txt" optional="true"
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40 label="Variables of interest (Optional)"
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41 help="variables not belonging to any block will not be considered"/>
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42 <!-- <param name="cutoff_comp" type="float" value="0.775" min="0" max="1"
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43 label="Cutoff comp"
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44 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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45 </inputs>
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46
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47 <outputs>
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48 <data name="output_rdata" format="rdata" label="${tool.name}_output.rdata" />
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49 <data name="output_response_var" format="tabular" label="${tool.name}_response_var.tsv" />
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50 <data name="output_blocks_comb" format="tabular" label="${tool.name}_blocks_comb.tsv" />
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51 </outputs>
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52
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53 <tests>
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54 </tests>
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55
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56 <help>
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57 </help>
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58
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59 </tool>