Mercurial > repos > workflow4metabolomics > isoplot
annotate isoplot.xml @ 2:61c959ebdef5 draft default tip
planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
author | workflow4metabolomics |
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date | Thu, 23 Jan 2025 15:28:29 +0000 |
parents | dd3e046a72ad |
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rev | line source |
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2
61c959ebdef5
planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents:
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changeset
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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
workflow4metabolomics
parents:
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changeset
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2 <macros> |
61c959ebdef5
planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents:
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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
workflow4metabolomics
parents:
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4 </macros> |
0
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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changeset
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5 <requirements> |
2
61c959ebdef5
planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents:
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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
workflow4metabolomics
parents:
1
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changeset
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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
workflow4metabolomics
parents:
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changeset
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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"
workflow4metabolomics
parents:
diff
changeset
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9 </requirements> |
2
61c959ebdef5
planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents:
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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
workflow4metabolomics
parents:
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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"
workflow4metabolomics
parents:
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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"
workflow4metabolomics
parents:
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13 #if $unstack: |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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14 -s |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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changeset
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15 #end if |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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16 #if $verbosity: |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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17 -v |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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changeset
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18 #end if |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
diff
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19 #if $annotation: |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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20 -a |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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21 #end if |
2
61c959ebdef5
planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents:
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22 -g > '$data_output' 2> '$log_output' |
0
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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changeset
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23 ]]></command> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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24 <inputs> |
1
dd3e046a72ad
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 97521f53202a392709ba96988129ae08d0dac317"
workflow4metabolomics
parents:
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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"
workflow4metabolomics
parents:
0
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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'/> |
0
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
diff
changeset
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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"
workflow4metabolomics
parents:
diff
changeset
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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"
workflow4metabolomics
parents:
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changeset
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29 <option value='pdf'>pdf</option> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
diff
changeset
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30 <option value='jpeg'>jpeg</option> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
diff
changeset
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31 <option value='png'>png</option> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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32 <option value='svg'>svg</option> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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33 <option value='html'>html</option> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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34 </param> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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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"
workflow4metabolomics
parents:
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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"
workflow4metabolomics
parents:
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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"
workflow4metabolomics
parents:
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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"
workflow4metabolomics
parents:
diff
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39 </param> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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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"
workflow4metabolomics
parents:
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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"
workflow4metabolomics
parents:
diff
changeset
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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"
workflow4metabolomics
parents:
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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"
workflow4metabolomics
parents:
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44 argument='-sa' optional='true'/>/--> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
diff
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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"
workflow4metabolomics
parents:
diff
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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"
workflow4metabolomics
parents:
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47 </section> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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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"
workflow4metabolomics
parents:
diff
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49 <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"
workflow4metabolomics
parents:
diff
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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"
workflow4metabolomics
parents:
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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"
workflow4metabolomics
parents:
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52 optional='true'/>--> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
diff
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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"
workflow4metabolomics
parents:
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54 </section> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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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"
workflow4metabolomics
parents:
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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"
workflow4metabolomics
parents:
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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"
workflow4metabolomics
parents:
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58 </inputs> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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59 |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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60 <outputs> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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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"
workflow4metabolomics
parents:
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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"
workflow4metabolomics
parents:
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63 <data name='log_output' format='txt' label='Run Info' /> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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64 </outputs> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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65 |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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66 <tests> |
2
61c959ebdef5
planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
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67 <test expect_test_failure="true"> |
0
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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68 <param name='datafile' value='input_data.csv' /> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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69 <param name='template_file' value='input_template.xlsx'/> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
diff
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70 <param name='format' value='pdf' /> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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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"
workflow4metabolomics
parents:
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72 <section name='SP' > |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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73 <param name='barplot' value='true' /> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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74 </section> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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75 <section name='IP' > |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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76 <param name='interactive_barplot' value='true' /> |
8b54f922377a
"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
workflow4metabolomics
parents:
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77 </section> |
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78 <output name='data_output' file='data_out.csv'/> |
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79 <output name='plots_output'> |
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80 <assert_contents> |
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81 <has_size value='2852573' delta='1000' /> |
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82 </assert_contents> |
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83 </output> |
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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' /> |
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87 </assert_contents> |
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88 </output> |
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89 </test> |
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90 </tests> |
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91 |
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92 <help><![CDATA[ |
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93 |
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94 .. class:: warningmark |
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95 |
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96 We strongly encourage you to read the `documentation <https://isoplot.readthedocs.io/en/latest/>`_ before using Isoplot. |
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97 |
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98 Isoplot2: Plotting isotopic labelling MS data |
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99 ============================================= |
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100 |
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101 **Positional arguments:** |
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102 |
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103 input_path Path to datafile |
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104 run_name Name of the current run |
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105 format Format of generated file |
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106 |
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107 **optional arguments:** |
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108 -h, --help show this help message and exit |
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109 --value Choices: "corrected_area", "isotopologue_fraction", "mean_enrichment". Select values to plot. This option can be given multiple times |
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110 |
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111 -m METABOLITE Metabolite(s) to plot. For all, type in 'all' |
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112 -c CONDITION Condition(s) to plot. For all, type in 'all' |
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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 |
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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> |
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132 <citations> |
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133 <citation type='bibtex'> |
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134 @misc{githubisoplot, |
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135 author = {Le Gregam, Loic}, |
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136 year = {2021}, |
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137 title = {isoplot}, |
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138 publisher = {GitHub}, |
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139 journal = {GitHub repository}, |
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140 url = {https://github.com/llegregam}, |
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141 }</citation> |
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142 </citations> |
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143 </tool> |