Mercurial > repos > ppericard > viscorvar

annotate circleCor.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="circleCor" name="circleCor" version="1.0" profile="16.04" workflow_compatible="true">
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3 <description>plots a correlation circle for the datasets whose correlation circles can be superimposed. This correlation circle contains the selected variables of these datasets which are included in a rectangle and the response 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="0.4">r-ellipse</requirement> -->
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8 <requirement type="package" version="2.0">r-argparse</requirement>
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9 <!-- <requirement type="package" version="1.1">r-rcolorbrewer</requirement> -->
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10
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11 <!-- <requirement type="package" version="6.8">bioconductor-mixomics</requirement> -->
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12 </requirements>
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13
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14 <stdio>
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15 <!-- <exit_code range="1:" level="fatal" /> -->
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16 </stdio>
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17
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18 <command detect_errors="aggressive">
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19 <![CDATA[
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20 Rscript
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21 ${__tool_directory__}/circleCor_wrapper.R
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22 --input_rdata ${input_rdata}
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23 --blocks_vec ${select_blocks.value}
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24 --responses_var ${select_responses_var}
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25 --x_min ${x_min}
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26 --x_max ${x_max}
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27 --y_min ${y_min}
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28 --y_max ${y_max}
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29 --output_var ${output_var}
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30 --output_pdf ${output_pdf}
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31 ]]>
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32 </command>
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33
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34 <inputs>
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35 <param name="input_rdata" type="data" format="rdata"
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36 label="Input RData file"
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37 help="output RData from matCorAddVar"/>
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38 <param name="blocks_vec_list" type="data" format="tabular"
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39 label="List of blocks vector."
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40 help="output *_blocks_comb.tsv file from matCorAddVar"/>
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41 <param name="select_blocks" type="select"
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42 label="Blocks"
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43 help="list of the blocks that are to be superimposed">
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44 <options from_dataset="blocks_vec_list">
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45 <column name="value" index="0"/>
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46 <filter type="unique_value" column="0"/>
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47 <filter type="sort_by" name="sorted_value" column="0"/>
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48 </options>
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49 </param>
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50 <param name="responses_var_list" type="data" format="tabular"
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51 label="List of response variables"
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52 help="output *_response_var.tsv file from matCorAddVar"/>
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53 <param name="select_responses_var" type="select" display="checkboxes"
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54 multiple="true" label="Response variables"
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55 help="select the response variables which will be plotted in the correlation circle">
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56 <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
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57 <options from_dataset="responses_var_list">
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58 <column name="value" index="0"/>
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59 <filter type="unique_value" column="0"/>
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60 <filter type="sort_by" name="sorted_value" column="0"/>
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61 </options>
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62 </param>
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63 <param name="x_min" type="float" value="-1" min="-1" max="1"
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64 label="X min" help="" />
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65 <param name="x_max" type="float" value="1" min="-1" max="1"
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66 label="X max" help="" />
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67 <param name="y_min" type="float" value="-1" min="-1" max="1"
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68 label="Y min" help="" />
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69 <param name="y_max" type="float" value="1" min="-1" max="1"
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70 label="Y max" help="" />
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71 </inputs>
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72
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73 <outputs>
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74 <data name="output_var" format="tabular" label="${tool.name}_selected_var.tsv" />
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75 <data name="output_pdf" format="pdf" label="${tool.name}.pdf" />
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76 </outputs>
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77
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78 <tests>
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79 </tests>
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80
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81 <help>
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82 </help>
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83
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84 </tool>