Mercurial > repos > ppericard > mixomics_blocksplsda

annotate networkVar.xml @ 4:b0ab97ffc2a1 draft

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
author ppericard
date Mon, 09 Mar 2020 11:53:32 -0400
parents 0a3c83f2197a
children bc28839b17fb
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1 <tool id="networkVar" name="networkVar" version="0.3.0" 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="6.8">bioconductor-mixomics</requirement>
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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 --block_splsda_rdata ${block_splsda_rdata}
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21 --var_list_file ${var_list_file}
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23 #if str($var_of_interest_file) !='':
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24 --interest_var_file ${var_of_interest_file}
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25 #end if
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27 --responses_var ${select_responses_var}
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29 --output_graph ${output_graph}
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30 ]]>
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31 </command>
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33 <inputs>
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34 <param name="mat_similarity_rdata" type="data" format="rdata"
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35 label="Input computeMatSimilarity RData file"
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36 help="output RData file from computeMatSimilarity"/>
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37 <param name="block_splsda_rdata" type="data" format="rdata"
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38 label="Input block.SPLSDA RData file"
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39 help="output Rdata file from block.SPLSDA"/>
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40 <param name="var_list_file" type="data" format="tabular"
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41 label="Variables list file"
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42 help="output tabular file from circleCor"/>
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43
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44 <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
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45 <param name="var_of_interest_file" type="data" format="tabular" optional="true"
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46 label="Variables of interest (Optional)"
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47 help="these variables have to belong to datasets that can be superimposed"/>
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48
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49 <param name="responses_var_list" type="data" format="txt"
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50 label="List of response variables"
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51 help="list of the response variables that will be in the network"/>
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52 <param name="select_responses_var" type="select" display="checkboxes" multiple="true"
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53 label="Response variables">
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54 <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
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55 <options from_dataset="responses_var_list">
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56 <column name="value" index="0"/>
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57 <filter type="unique_value" column="0"/>
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58 <filter type="sort_by" name="sorted_value" column="0"/>
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59 </options>
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60 </param>
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61 </inputs>
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63 <outputs>
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64 <data name="output_graph" format="xml" label="${tool.name}_graph.graphml" />
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65 </outputs>
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67 <tests>
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68 </tests>
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70 <help>
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71 </help>
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73 </tool>