Mercurial > repos > mvdbeek > plot_correlation_matrix

annotate plot_corr.xml @ 0:0cee38fb62af draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
author mvdbeek
date Fri, 27 Apr 2018 09:48:24 -0400
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0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
mvdbeek
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1 <tool id="plot_correlation" name="Plot correlations" version="0.1.3">
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
mvdbeek
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2 <description>for multiple samples</description>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
mvdbeek
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3 <requirements>
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mvdbeek
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4 <requirement type="package" version="0.8.1">seaborn</requirement>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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5 <requirement type="package" version="6.7">click</requirement>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
mvdbeek
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8 python '$__tool_directory__/plot_corr.py'
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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9 #echo "".join(["'%s' " % f for f in $input_files])
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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10 -c $c
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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11 --labels '$labels'
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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12 #if $plot_type != "None"
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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13 --plot_path output.$plot_type
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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14 #end if
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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15 --correlation_matrix_path $tab_output
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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16 --method $method
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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17 --skiprows $skiprows
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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18 #if $input_files[0].ext == 'csv'
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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19 --sep ","
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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20 #end if
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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21 #if $plot_type != "None"
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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22 && mv output.$plot_type plot
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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23 #end if
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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24 ]]></command>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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25 <configfiles>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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26 <configfile name="labels">#for f in $input_files
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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27 $f.element_identifier
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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28 #end for</configfile>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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29 </configfiles>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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30 <inputs>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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31 <param name="input_files" type="data" multiple="true" format="tabular,csv" label="Select the files for which to calculate the correlation"/>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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32 <param argument="-c" type="data_column" data_ref="input_files" value="1" label="Select the numeric column to use"/>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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33 <param argument="--skiprows" type="integer" min="0" value="0" label="Skip the first N rows" help="Make sure that all values are numeric"/>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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34 <param argument="--plot_type" type="select" label="Select the type of plot to produce">
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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35 <option value="pdf">PDF</option>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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36 <option value="png">PNG</option>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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37 <option value="None">Don't output plot</option>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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38 </param>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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39 <param argument="--method" type="select" label="Select the correlation method">
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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40 <option value="pearson">Pearson Correlation</option>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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41 <option value="spearman">Spearman Correlation</option>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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42 <option value="kendall">Kendall-Tau Correlation</option>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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43 </param>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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44 </inputs>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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45 <outputs>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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46 <data name="plot_output" format="pdf" from_work_dir="plot" label="${tool.name} plot on ${on_string}">
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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47 <filter>str(plot_type) != "None"</filter>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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48 <change_format>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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49 <when input="plot_type" value="png" format="png"/>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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50 </change_format>
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51 </data>
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52 <data name="tab_output" format="tabular" label="${tool.name} table on ${on_string}"/>
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="input_files" value="1.txt,2.txt,3.txt" ftype="tabular"/>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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57 <output name="plot_output" value="corr.pdf" ftype="pdf"/>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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58 <output name="tab_output" value="corr.tab" ftype="tabular"/>
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59 </test>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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60 <test>
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61 <param name="input_files" value="1.txt,2.txt,3.txt" ftype="tabular"/>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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62 <param name="plot_type" value="png"/>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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63 <output name="plot_output" value="corr.png" ftype="png"/>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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64 <output name="tab_output" value="corr.tab" ftype="tabular"/>
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65 </test>
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66 </tests>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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67 <help><![CDATA[
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68 What it does
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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69 ------------
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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70
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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71 This tool calculates the correlation for a selected colum across many datasets.
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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72
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73 Example output:
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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74 ---------------
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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75
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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76 .. image:: $PATH_TO_IMAGES/corr.png
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77
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78 ]]></help>
0cee38fb62af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496
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79 </tool>