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"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 97521f53202a392709ba96988129ae08d0dac317"
author workflow4metabolomics
date Mon, 04 Oct 2021 09:01:32 +0000
parents 8b54f922377a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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dd3e046a72ad "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 97521f53202a392709ba96988129ae08d0dac317"
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1 <tool id='isoplot' name='Isoplot: Generate plots from isocor output' version='1.3.0+galaxy1' profile='20.01'>
0
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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2 <requirements>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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3 <requirement type='package' version='1.3.0'>isoplot</requirement>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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4 </requirements>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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5 <command><![CDATA[
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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6 isoplot '$datafile' 'galaxy' '$format' --value '$value' --template '$template_file' $SP.barplot $SP.meaned_barplot
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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7 $SP.static_heatmap $SP.static_clustermap $IP.interactive_barplot $IP.interactive_meanplot $IP.interactive_heatmap
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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8 #if $unstack:
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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9 -s
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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10 #end if
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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11 #if $verbosity:
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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12 -v
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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13 #end if
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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14 #if $annotation:
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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15 -a
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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16 #end if
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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17 -g -z '$plots_output' > $data_output 2> '$log_output'
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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18 ]]></command>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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19 <inputs>
1
dd3e046a72ad "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 97521f53202a392709ba96988129ae08d0dac317"
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20 <param name='datafile' type='data' format='csv,tabular' multiple='true' label='Upload data that has been corrected by Isocor (.tsv format)' />
dd3e046a72ad "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 97521f53202a392709ba96988129ae08d0dac317"
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21 <param name='template_file' type='data' format='csv,xlsx' multiple='true' label='Upload template file containing plot metadata (.xlsx format)' argument='--template'/>
0
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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22 <!--param name='run_name' type='text' label='Run name' /-->
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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23 <param name='format' type='select' label='Plot format'>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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24 <option value='pdf'>pdf</option>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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25 <option value='jpeg'>jpeg</option>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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26 <option value='png'>png</option>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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27 <option value='svg'>svg</option>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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28 <option value='html'>html</option>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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29 </param>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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30 <param name='value' type='select' label='Data to plot' >
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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31 <option value='corrected_area'>Corrected Area</option>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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32 <option value='isotopologue_fraction'>Isotopologue Fraction</option>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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33 <option value='mean_enrichment'>Mean Enrichment</option>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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34 </param>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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35 <section name='SP' title='Select static plots to generate'>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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36 <param type='boolean' argument='--barplot' label='Flag to generate barplots' truevalue='-bp' falsevalue=''/>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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37 <param type='boolean' argument='--meaned_barplot' label='Flag to generate meaned barplots' truevalue='-mb' falsevalue=''/>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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38 <!--<param type='boolean' name='generate_areaplot' label='Flag to generate stacked area plots'
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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39 argument='-sa' optional='true'/>/-->
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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40 <param type='boolean' argument='--static_heatmap' label='Flag to generate heatmap' truevalue='-hm' falsevalue=''/>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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41 <param type='boolean' argument='--static_clustermap' label='Flag to generate clustermap' truevalue='-cm' falsevalue=''/>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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42 </section>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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43 <section name='IP' title='Select interactive plots to generate'>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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44 <param type='boolean' argument='--interactive_barplot' label='Flag to generate barplots' truevalue='-IB' falsevalue=''/>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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45 <param type='boolean' argument='--interactive_meanplot' label='Flag to generate meaned barplots' truevalue='-IM' falsevalue=''/>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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46 <!-- <param type='boolean' name='generate_areaplot' label='Flag to generate stacked area plots' argument='-IS'
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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47 optional='true'/>-->
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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48 <param type='boolean' argument='--interactive_heatmap' label='Flag to generate heatmap' truevalue='-HM' falsevalue=''/>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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49 </section>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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50 <param type='boolean' name='unstack' label='Flag to unstack bars in barplots' truevalue='-s' falsevalue=''/>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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51 <param type='boolean' name='verbosity' label='Flag to get debug information' truevalue='-v' falsevalue=''/>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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52 <param type='boolean' name='annotation' label='Flag to add annotations on the maps' truevalue='-a' falsevalue=''/>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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53 </inputs>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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54
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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55 <outputs>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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56 <data name='data_output' format='csv' label='Formatted data used for plotting' />
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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57 <data name='plots_output' format='zip' label='Resulting plots' />
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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58 <data name='log_output' format='txt' label='Run Info' />
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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59 </outputs>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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60
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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61 <tests>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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62 <test>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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63 <param name='datafile' value='input_data.csv' />
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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64 <param name='template_file' value='input_template.xlsx'/>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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65 <param name='format' value='pdf' />
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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66 <param name='value' value='isotopologue_fraction' />
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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67 <section name='SP' >
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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68 <param name='barplot' value='true' />
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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69 </section>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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70 <section name='IP' >
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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71 <param name='interactive_barplot' value='true' />
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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72 </section>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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73 <output name='data_output' file='data_out.csv'/>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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74 <output name='plots_output'>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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75 <assert_contents>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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76 <has_size value='2852573' delta='1000' />
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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77 </assert_contents>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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78 </output>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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79 <output name='log_output'>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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80 <assert_contents>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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81 <has_text text='- isoplot_log.main.cli_process - INFO - Plots created. Run is terminated' />
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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82 </assert_contents>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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83 </output>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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84 </test>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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85 </tests>
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86
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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87 <help><![CDATA[
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88
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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89 .. class:: warningmark
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90
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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91 We strongly encourage you to read the `documentation <https://isoplot.readthedocs.io/en/latest/>`_ before using Isoplot.
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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92
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93 Isoplot2: Plotting isotopic labelling MS data
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94 =============================================
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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95
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96 **Positional arguments:**
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97
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98 input_path Path to datafile
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99 run_name Name of the current run
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100 format Format of generated file
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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101
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102 **optional arguments:**
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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103 -h, --help show this help message and exit
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104 --value Choices: "corrected_area", "isotopologue_fraction", "mean_enrichment". Select values to plot. This option can be given multiple times
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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105
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106 -m METABOLITE Metabolite(s) to plot. For all, type in 'all'
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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107 -c CONDITION Condition(s) to plot. For all, type in 'all'
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108 -t TIME Time(s) to plot. For all, type in 'all'
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109 -tp, --template TEMPLATE_PATH Path to template file
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110
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111 -sa, --stacked_areaplot Create static stacked areaplot
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112 -bp, --barplot Create static barplot
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113 -mb, --meaned_barplot Create static barplot with meaned replicates
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114
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115 -IB, --interactive_barplot Create interactive stacked barplot
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116 -IM, --interactive_stacked_meanplot Create interactive stacked barplot with meaned replicates
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117 -IS, --interactive_areaplot Create interactive stacked areaplot
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118 -hm, --static_heatmap Create a static heatmap using mean enrichment data
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119 -cm, --static_clustermap Create a static heatmap with clustering using mean enrichment data
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120 -HM, --interactive_heatmap Create interactive heatmap using mean enrichment data
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121
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122 -s, --stack Add option if barplots should be unstacked
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123 -v, --verbose Turns logger to debug mode
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124 -a, --annot Add option if annotations should be added on maps
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125
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126 ]]></help>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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127 <citations>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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128 <citation type='bibtex'>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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129 @misc{githubisoplot,
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130 author = {Le Gregam, Loic},
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131 year = {2021},
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132 title = {isoplot},
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133 publisher = {GitHub},
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134 journal = {GitHub repository},
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135 url = {https://github.com/llegregam},
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136 }</citation>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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137 </citations>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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138 </tool>