Mercurial > repos > ppericard > viscorvar

annotate networkVar.xml @ 0:d0b77b926863 draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
author ppericard
date Tue, 23 Jun 2020 19:57:35 -0400
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children e93350dc99f1
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1 <tool id="networkVar" name="networkVar" version="1.0" profile="16.04" workflow_compatible="true">
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3 <description>creates a network between selected variables of datasets and the response variables. In the network, the similarity between two variables is associated with the link between these two variables.</description>
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5 <requirements>
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6 <requirement type="package" version="6.12">bioconductor-mixomics</requirement> <!-- Remove when viscorvar is available via conda -->
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7 <requirement type="package" version="1.2">r-igraph</requirement>
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8 <requirement type="package" version="2.0">r-argparse</requirement>
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9 </requirements>
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11 <stdio>
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12 <!-- <exit_code range="1:" level="fatal" /> -->
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13 </stdio>
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15 <command detect_errors="aggressive">
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16 <![CDATA[
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17 Rscript
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18 ${__tool_directory__}/networkVar_wrapper.R
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19 --mat_similarity_rdata ${mat_similarity_rdata}
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20 --var_list_file ${var_list_file}
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21 --response_var ${select_response_var}
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22 --output_graph ${output_graph}
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23 ]]>
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24 </command>
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26 <inputs>
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27 <param name="mat_similarity_rdata" type="data" format="rdata"
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28 label="Input computeMatSimilarity RData file"
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29 help="output RData file from computeMatSimilarity"/>
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30 <param name="var_list_file" type="data" format="tabular"
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31 label="Variables list file"
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32 help="selected variables output tabular file from circleCor"/>
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33
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34 <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
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35 <!-- <param name="var_of_interest_file" type="data" format="txt" optional="true"
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36 label="Variables of interest (Optional)"
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37 help="these variables have to belong to datasets that can be superimposed"/> -->
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38
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39 <param name="response_var_list" type="data" format="tabular"
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40 label="List of response variables"
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41 help="output *_response_var.tsv file from matCorAddVar"/>
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42 <param name="select_response_var" type="select" display="checkboxes" multiple="true"
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43 label="Response variables"
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44 help="response variables that will be plotted in the network">
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45 <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
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46 <options from_dataset="response_var_list">
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47 <column name="value" index="0"/>
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48 <filter type="unique_value" column="0"/>
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49 <filter type="sort_by" name="sorted_value" column="0"/>
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50 </options>
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51 </param>
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52 </inputs>
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53
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54 <outputs>
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55 <data name="output_graph" format="xml" label="${tool.name}_graph.graphml" />
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56 </outputs>
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57
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58 <tests>
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59 </tests>
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61 <help>
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62 </help>
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64 </tool>