annotate isoplot.xml @ 2:61c959ebdef5 draft default tip

planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
author workflow4metabolomics
date Thu, 23 Jan 2025 15:28:29 +0000
parents dd3e046a72ad
children
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61c959ebdef5 planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
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1 <tool id='isoplot' name='Isoplot: Generate plots from isocor output' version='@TOOL_VERSION@+galaxy2' profile='20.01'>
61c959ebdef5 planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
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2 <macros>
61c959ebdef5 planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
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3 <token name="@TOOL_VERSION@">1.3.1</token>
61c959ebdef5 planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
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4 </macros>
0
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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5 <requirements>
2
61c959ebdef5 planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
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6 <requirement type='package' version='3.0.3'>jinja2</requirement>
61c959ebdef5 planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
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7 <requirement type='package' version='1.3.1'>zlib</requirement>
61c959ebdef5 planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
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8 <requirement type='package' version='@TOOL_VERSION@'>isoplot</requirement>
0
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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9 </requirements>
2
61c959ebdef5 planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
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10 <command detect_errors="exit_code"><![CDATA[
61c959ebdef5 planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
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11 isoplot '$datafile' 'galaxy' '$format' --value '$value' --template '$template_file' --zip '$plots_output' $SP.barplot $SP.meaned_barplot
0
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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12 $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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13 #if $unstack:
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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14 -s
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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15 #end if
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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16 #if $verbosity:
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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17 -v
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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18 #end if
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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19 #if $annotation:
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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20 -a
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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21 #end if
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61c959ebdef5 planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
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22 -g > '$data_output' 2> '$log_output'
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23 ]]></command>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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24 <inputs>
1
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25 <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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26 <param name='template_file' type='data' format='csv,xlsx' multiple='true' label='Upload template file containing plot metadata (.xlsx format)' argument='--template'/>
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27 <!--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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28 <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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29 <option value='pdf'>pdf</option>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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30 <option value='jpeg'>jpeg</option>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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31 <option value='png'>png</option>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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32 <option value='svg'>svg</option>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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33 <option value='html'>html</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 <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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36 <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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37 <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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38 <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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39 </param>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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40 <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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41 <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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42 <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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43 <!--<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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44 argument='-sa' optional='true'/>/-->
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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45 <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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46 <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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47 </section>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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48 <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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49 <param type='boolean' argument='--interactive_barplot' label='Flag to generate barplots' truevalue='-IB' falsevalue=''/>
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50 <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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51 <!-- <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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52 optional='true'/>-->
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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53 <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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54 </section>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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55 <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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56 <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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57 <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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58 </inputs>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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59
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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60 <outputs>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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61 <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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62 <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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63 <data name='log_output' format='txt' label='Run Info' />
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64 </outputs>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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65
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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66 <tests>
2
61c959ebdef5 planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
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67 <test expect_test_failure="true">
0
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68 <param name='datafile' value='input_data.csv' />
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69 <param name='template_file' value='input_template.xlsx'/>
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70 <param name='format' value='pdf' />
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71 <param name='value' value='isotopologue_fraction' />
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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72 <section name='SP' >
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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73 <param name='barplot' value='true' />
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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74 </section>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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75 <section name='IP' >
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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76 <param name='interactive_barplot' value='true' />
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77 </section>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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78 <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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79 <output name='plots_output'>
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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_size value='2852573' delta='1000' />
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82 </assert_contents>
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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 <output name='log_output'>
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85 <assert_contents>
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86 <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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87 </assert_contents>
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88 </output>
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89 </test>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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90 </tests>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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91
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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92 <help><![CDATA[
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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93
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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94 .. class:: warningmark
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95
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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96 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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97
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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98 Isoplot2: Plotting isotopic labelling MS data
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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99 =============================================
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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100
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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101 **Positional arguments:**
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102
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103 input_path Path to datafile
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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104 run_name Name of the current run
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105 format Format of generated file
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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106
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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107 **optional arguments:**
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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108 -h, --help show this help message and exit
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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109 --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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110
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111 -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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112 -c CONDITION Condition(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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113 -t TIME Time(s) to plot. For all, type in 'all'
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114 -tp, --template TEMPLATE_PATH Path to template file
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115
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116 -sa, --stacked_areaplot Create static stacked areaplot
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117 -bp, --barplot Create static barplot
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118 -mb, --meaned_barplot Create static barplot with meaned replicates
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119
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120 -IB, --interactive_barplot Create interactive stacked barplot
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121 -IM, --interactive_stacked_meanplot Create interactive stacked barplot with meaned replicates
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122 -IS, --interactive_areaplot Create interactive stacked areaplot
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123 -hm, --static_heatmap Create a static heatmap using mean enrichment data
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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124 -cm, --static_clustermap Create a static heatmap with clustering using mean enrichment data
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125 -HM, --interactive_heatmap Create interactive heatmap using mean enrichment data
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126
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127 -s, --stack Add option if barplots should be unstacked
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128 -v, --verbose Turns logger to debug mode
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129 -a, --annot Add option if annotations should be added on maps
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130
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131 ]]></help>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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132 <citations>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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133 <citation type='bibtex'>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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134 @misc{githubisoplot,
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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135 author = {Le Gregam, Loic},
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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136 year = {2021},
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137 title = {isoplot},
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138 publisher = {GitHub},
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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139 journal = {GitHub repository},
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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140 url = {https://github.com/llegregam},
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141 }</citation>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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142 </citations>
8b54f922377a "planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
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143 </tool>