Mercurial > repos > iuc > dimet_enrichment_plot

annotate dimet_enrichment_plot.xml @ 1:74599e075574 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 6da96d865a3a557cfa3ad09e1cfa830519e73748
author iuc
date Tue, 06 Aug 2024 17:28:59 +0000
parents 1bfe9f9608e4
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1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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1 <tool id="dimet_@EXECUTABLE@" name="dimet @TOOL_LABEL@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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2 <description>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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3 Figures of mean enrichment by metabolite, as line-plots (by DIMet)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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4 </description>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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5 <macros>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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6 <token name="@TOOL_LABEL@">enrichment plot</token>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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7 <token name="@EXECUTABLE@">enrichment_plot</token>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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8 <import>macros.xml</import>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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9 </macros>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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10 <expand macro="requirements"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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11 <command detect_errors="exit_code"><![CDATA[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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12 @INIT_CONFIG@
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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13 @INIT_ENRICHMENT_PLOT@
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14 @INIT_PLOT_CONDITIONS@
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15 @INIT_TIMEPOINTS@
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16 @INIT_ENRICHMENT_METABOLITES@
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17 HYDRA_FULL_ERROR=1 python -m dimet
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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18 '++hydra.run.dir=.'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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19 '++figure_path=figures'
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20 '++table_path=tables'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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21 '++analysis={
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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22 metabolites:${metabolites},
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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23 dataset:{
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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24 _target_:dimet.data.DatasetConfig,
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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25 name: "Galaxy DIMet run"
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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26 },
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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27 method:{
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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28 _target_: dimet.method.MeanEnrichmentLinePlotConfig,
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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29 label: mean_enrichment_line_plot,
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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30 name: "Generate mean enrichment line plots",
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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31 palette_condition: ${output_options.palette},
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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32 palette_metabolite: auto_multi_color,
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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33 xaxis_title: ${output_options.xaxis_title},
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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34 alpha: ${output_options.alpha},
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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35 plot_grouped_by_dict: null,
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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36 color_lines_by: '${output_options.color_lines_by}',
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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37 height_subplot: ${output_options.height_subplot},
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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38 figure_format:${output_options.figure_format},
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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39 as_grid:${output_options.as_grid}
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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40 },
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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41 width_subplot: '${output_options.width_subplot}',
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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42 label: enrich_lineplot
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43 }'
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44 '++analysis.dataset.label='
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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45 '++analysis.timepoints=${timepoints}'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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46 '++analysis.dataset.subfolder='
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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47 '++analysis.dataset.conditions=${conditions}'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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48
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49 #if $metadata_path:
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50 '++analysis.dataset.metadata=metadata'
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51 #end if
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52 #if $me_or_frac_contrib_file:
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53 '++analysis.dataset.mean_enrichment=me_or_frac_contrib'
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54 #end if
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55 @REMOVE_CONFIG@
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56 ]]></command>
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57 <inputs>
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58 <expand macro="input_parameters_enrichment"/>
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59 <expand macro="plot_factor_list"/>
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60 <expand macro="timepoint"/>
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61 <expand macro="compartments_enrichment"/>
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62 <expand macro="enrichment_metabolites_list"/>
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63 <section name="output_options" title="Output options">
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64 <param name="figure_format" type="select" value="pdf" display="radio" label="Select output figure format" help="Please enter at max 1 format">
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65 <option value="pdf">Pdf</option>
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66 <option value="svg">Svg</option>
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67 </param>
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68 <expand macro="palette"/>
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69 <param name="color_lines_by" type="select" value="condition" display="radio" label="Select color for lines" help="Please enter at max 1 format">
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70 <option value="condition">Condition</option>
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71 <option value="metabolite">Metabolite</option>
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72 </param>
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73 <param name="alpha" type="float" min="0.0" max="1.0" value="1.0" label="alpha of subfig plots"
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74 help="Default value is 1."/>
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75 <param name="height_subplot" type="float" min="1.0" max="15.0" value="6.4" label="height of subfig plots"
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76 help="Default value is 3."/>
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77 <param name="width_subplot" type="float" min="1.0" max="15.0" value="4.0" label="width of subfig plots"
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78 help="Default value is 3."/>
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79 <param name="as_grid" type="boolean" value="false" label="plot as grid"
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80 help="Default value is false."/>
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81 <param name="xaxis_title" type="text" value="Time" optional="false" label="xaxis_title to add to output files" >
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82 <sanitizer invalid_char="">
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83 <valid initial="string.ascii_letters,string.digits">
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84 <add value="_" />
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85 </valid>
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86 </sanitizer>
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87 </param>
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88 </section>
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89 </inputs>
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90
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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91 <outputs>
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92 <collection name="report" type="list">
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93 <discover_datasets pattern="__designation_and_ext__" directory="figures"/>
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94 </collection>
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95 </outputs>
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96 <tests>
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97 <test>
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98 <param name="me_or_frac_contrib_file" ftype="tabular" value="FracContribution_C.csv"/>
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99 <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/>
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100 <repeat name="plot_factor_list">
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101 <param name="condition" value="Control"/>
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102 </repeat>
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103 <repeat name="plot_factor_list">
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104 <param name="condition" value="L-Cycloserine"/>
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105 </repeat>
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106 <param name="timepoint" value='T0,T2h'/>
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107 <param name="compartments" value='cell,med'/>
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108 <param name="metabolites_list" value="Fumaric_acid,Glycine,L-Proline"/>
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109 <section name="output_options">
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110 <param name="alpha" value="1.0"/>
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111 <param name="height_subplot" value="6.4"/>
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112 <param name="width_subplot" value="4.0"/>
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113 <param name="xaxis_title" value="Time"/>
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114 <param name="color_lines_by" value="condition"/>
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115 <param name="figure_format" value="svg"/>
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116 </section>
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117
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118 <output_collection name="report" type="list" count="6">
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119 <element file="mean_enrichment-cell-Fumaric_acid.svg" name="mean_enrichment-cell-Fumaric_acid" ftype="svg" compare="sim_size" delta="100"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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120 <element file="mean_enrichment-cell-Glycine.svg" name="mean_enrichment-cell-Glycine" ftype="svg" compare="sim_size" delta="100"/>
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121 <element file="mean_enrichment-cell-L-Proline.svg" name="mean_enrichment-cell-L-Proline" ftype="svg" compare="sim_size" delta="100"/>
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122 <element file="mean_enrichment-med-Fumaric_acid.svg" name="mean_enrichment-med-Fumaric_acid" ftype="svg" compare="sim_size" delta="100"/>
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123 <element file="mean_enrichment-med-Glycine.svg" name="mean_enrichment-med-Glycine" ftype="svg" compare="sim_size" delta="100"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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124 <element file="mean_enrichment-med-L-Proline.svg" name="mean_enrichment-med-L-Proline" ftype="svg" compare="sim_size" delta="100"/>
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125 </output_collection>
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126 </test>
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127 </tests>
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128 <help><![CDATA[
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129 This module is part of DIMet: Differential analysis of Isotope-labeled targeted Metabolomics data (https://pypi.org/project/DIMet/).
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130
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131 DIMet enrichment plot performs line-plot figures for visualization of the (stable isotope) mean enrichment across all the time points present in your data, for each metabolite. All (or selected) metabolites are processed automatically.
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132
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133 The figures in .pdf format are of publication quality, and as they are vectorial images you can open them and customize aesthetics with a professional image software such as Inkscape, Adobe Illustrator, Sketch, CorelDRAW, etc.
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134
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135
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136 **Input data files**
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137
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138 For running DIMet @EXECUTABLE@ you need the following .csv files :
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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139
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140 - The mean **enrichment** file, and
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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141
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142 - The metadata file, a unique file with the description of the samples. This file is compulsory (see section **Metadata File Information**).
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143
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144
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145 The mean enrichment file must be organized as a matrix:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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146
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147 - The first column must contain Metabolite IDs that are unique (not repeated) within the file.
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148
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149 - The rest of the columns correspond to the samples
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150
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151 - The rows correspond to the metabolites
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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152
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153 - The values must be tab separated, with the first row containing the sample/column labels.
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154
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155
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156 Example - mean **enrichment** or labeled fractional contributions:
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157
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158 =============== ================== ================== ================== ================== ================== ==================
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159 ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06**
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160 =============== ================== ================== ================== ================== ================== ==================
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161 2_3-PG 0.9711 0.968 0.9909 0.991 0.40 0.9
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162 2-OHGLu 0.01719 0.0246 0.554 0.555 0.73 0.68
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163 Glc6P 0.06 0.66 2683 0.06 2068 2172
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164 Gly3P 0.06 0.06 0.06 1 5 3
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165 IsoCit 0.06 1 0.49 0.36 6 10
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166 =============== ================== ================== ================== ================== ================== ==================
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167
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168
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169
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170 **Metadata File Information**
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171
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172 Provide a tab-separated file that has the names of the samples in the first column and one header row.
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173 Column names must be exactly in this order:
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174
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175 name_to_plot
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176 condition
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177 timepoint
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178 timenum
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179 compartment
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180 original_name
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181
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182
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183 Example **Metadata File**:
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184
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185
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186 ==================== =============== ============= ============ ================ =================
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187 **name_to_plot** **condition** **timepoint** **timenum** **compartment** **original_name**
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188 -------------------- --------------- ------------- ------------ ---------------- -----------------
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189 Control_cell_T0-1 Control T0 0 cell MCF001089_TD01
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190 Control_cell_T0-2 Control T0 0 cell MCF001089_TD02
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191 Control_cell_T0-3 Control T0 0 cell MCF001089_TD03
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192 Tumoral_cell_T0-1 Tumoral T0 0 cell MCF001089_TD04
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193 Tumoral_cell_T0-2 Tumoral T0 0 cell MCF001089_TD05
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194 Tumoral_cell_T0-3 Tumoral T0 0 cell MCF001089_TD06
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195 Tumoral_cell_T24-1 Tumoral T24 24 cell MCF001089_TD07
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196 Tumoral_cell_T24-2 Tumoral T24 24 cell MCF001089_TD08
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197 Tumoral_cell_T24-3 Tumoral T24 24 cell MCF001090_TD01
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198 Control_med_T24-1 Control T24 24 med MCF001090_TD02
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199 Control_med_T24-2 Control T24 24 med MCF001090_TD03
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200 Tumoral_med_T24-1 Tumoral T24 24 med MCF001090_TD04
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201 Tumoral_med_T24-2 Tumoral T24 24 med MCF001090_TD05
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202 Control_med_T0-1 Control T0 0 med MCF001090_TD06
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203 Tumoral_med_T0-1 Tumoral T0 0 med MCF001090_TD07
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204 Tumoral_med_T0-2 Tumoral T0 0 med MCF001090_TD08
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205 ==================== =============== ============= ============ ================ =================
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206
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207
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208 The column **original_name** must have the names of the samples as given in your data.
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209
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210 The column **name_to_plot** must have the names as you want them to be (or set identical to original_name if you prefer). To set names that
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211 are meaningful is a better choice, as we will take them to display the results.
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212
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213 The column **timenum** must contain only the numeric part of the timepoint, for example 2,0, 10, 100 (this means, without letters ("T", "t", "s", "h" etc)
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214 nor any other symbol). Make sure these time numbers are in the same units (but do not write the units here!).
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215
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216 The column **compartment** is an abbreviation, coined by you, for the compartments. This will be used for the results' files names: the longer the
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217 compartments names are, the longer the output files' names! Please pick short and clear abbreviations to fill this column.
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218
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219
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220 **Running the analysis**
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221
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222
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223 You can precise how you want your analysis to be executed, with the parameters:
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224
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225 - **conditions**: the conditions present in your data, exactly in the ORDER you want them to appear in the legend of each figure.
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226
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227 - **width_subplot** : the desired width (in inches) for the the individual metabolites' figures
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228
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229 There exist hints on use that will guide you, next to the parameters.
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230
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231 Note that this plot makes sense when you dispose of two or more time-points. If your setup is not a time-series, you may rather use our metabologram integration with the differential mean enrichment (comparing the conditions of your choice).
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232
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233 The output consists of line-plot figures, one by each metabolite.
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234
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235 **Available data for testing**
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236
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237 You can test our tool with the data from our manuscript https://zenodo.org/record/10579862 (the pertinent
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238 files for you are located in the subfolders inside the data folder).
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239 You can also use the minimal data examples from https://zenodo.org/record/10579891
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240
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241 ]]>
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242 </help>
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243 <expand macro="citations"/>
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244 </tool>