Mercurial > repos > iuc > dimet_isotopologues_plot

annotate dimet_isotopologues_plot.xml @ 6:a7d1d77e7cc3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
author iuc
date Fri, 21 Jun 2024 18:54:57 +0000
parents 89ca62980a2e
children
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1 <tool id="dimet_@EXECUTABLE@" name="dimet @TOOL_LABEL@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description>
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3 Figures of isotopologues proportions by metabolite, as stacked barplots (by DIMet)
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4 </description>
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5 <macros>
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6 <token name="@TOOL_LABEL@">isotopologues plot</token>
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7 <token name="@EXECUTABLE@">isotopologues_plot</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements"/>
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11 <command detect_errors="exit_code"><![CDATA[
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12 @INIT_CONFIG@
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13 @INIT_ISOTOPOLOGUE_PLOT@
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14 @INIT_PLOT_CONDITIONS@
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15 @INIT_TIMEPOINTS@
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16 HYDRA_FULL_ERROR=1 python -m dimet
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17 '++hydra.run.dir=.'
0
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18 '++figure_path=figures'
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19 '++table_path=tables'
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20 '++analysis={
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21 dataset:{
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22 _target_:dimet.data.DatasetConfig,
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23 name: "Galaxy DIMet run"
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24 },
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25 method:{
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26 _target_: dimet.method.IsotopologueProportionsPlotConfig,
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27 label: isotopologue_proportions_plot,
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28 name: "Generate isotopologues proportion plots",
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29 barcolor: timepoint,
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30 axisx: condition,
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31 max_nb_carbons_possible: '${output_options.max_nb_carbons_possible}',
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32 appearance_separated_time: '${output_options.appearance_separated_time}', ## adds a space between timepoints, conditions stay comparative
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33 split_plots_by_condition: '${output_options.split_plots_by_condition}', ## prints each condition in independent plots
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34 x_ticks_text_size: ${output_options.x_ticks_text_size},
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35 y_ticks_text_size: ${output_options.y_ticks_text_size},
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36 as_grid: ${output_options.as_grid},
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37 figure_format:${output_options.figure_format},
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38 sharey:${output_options.sharey}
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39 },
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40 label: isotopologue_proportions_plot
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41 }'
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42 '++analysis.dataset.label='
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43 '++analysis.timepoints=${timepoints}'
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44 '++analysis.inner_numbers_size='${output_options.inner_numbers_size}''
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45 '++analysis.width_each_stack='${output_options.width_each_stack}''
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46 '++analysis.method.height_each_stack='${output_options.height_each_stack}''
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47 '++analysis.dataset.subfolder='
2
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48 '++analysis.dataset.conditions=${conditions}'
0
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49 '++x_text='metabolites''
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50
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51 #if $metadata_path:
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52 '++analysis.dataset.metadata=metadata'
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53 #end if
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54 #if $isotop_prop_file:
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55 '++analysis.dataset.isotopologue_proportions=isotop_prop'
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56 #end if
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57 @REMOVE_CONFIG@
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58 ]]></command>
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59 <inputs>
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60 <expand macro="input_parameters_isotopologue"/>
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61 <expand macro="plot_factor_list"/>
0
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62 <expand macro="timepoint"/>
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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 <param name="appearance_separated_time" type="boolean" value="false" label="appearance separated time"
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69 help="Default value is false."/>
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70 <param name="split_plots_by_condition" type="boolean" value="false" label="split plots by condition"
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71 help="Default value is false."/>
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72 <param name="as_grid" type="boolean" value="false" label="plot as grid"
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73 help="Default value is false."/>
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74 <param name="sharey" type="boolean" value="false" label="share y axis"
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75 help="Default value is false."/>
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76 <param name="x_ticks_text_size" type="integer" min="1" max="24" value="18" label="xticks text size"
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77 help="Default value is 18."/>
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78 <param name="y_ticks_text_size" type="integer" min="1" max="24" value="18" label="yticks text size"
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79 help="Default value is 18."/>
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80 <param name="height_each_stack" type="float" min="1.0" max="10.0" value="4.6" label="height of each stack"
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81 help="Default value is 4.6."/>
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82 <param name="width_each_stack" type="float" min="0.1" max="5.0" value="3.0" label="width of each stack"
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83 help="Default value is 3.0."/>
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84 <param name="inner_numbers_size" type="integer" min="1" max="20" value="13" label="inner number size"
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85 help="Default value is 13."/>
5
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86 <param name="max_nb_carbons_possible" type="integer" min="1" max="30" value="12" label="max number carbons possible"
0
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87 help="Default value is 12."/>
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88 </section>
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89 </inputs>
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90
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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="metadata_path" ftype="tabular" value="example2_metadata.csv"/>
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99 <param name="isotop_prop_file" ftype="tabular" value="CorrectedIsotopologues_reduced.csv"/>
2
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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>
0
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106 <param name="timepoint" value='T0,T2h'/>
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107 <section name="output_options">
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108 <param name="figure_format" value="svg"/>
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109 <param name="appearance_separated_time" value="false"/>
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110 <param name="split_plots_by_condition" value="false"/>
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111 <param name="as_grid" value="false"/>
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112 <param name="sharey" value="false"/>
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113 <param name="inner_numbers_size" value="13"/>
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114 <param name="max_nb_carbons_possible" value="12"/>
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115 <param name="width_each_stack" value="3.0"/>
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116 <param name="height_each_stack" value="4.6"/>
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117 <param name="x_ticks_text_size" value="18"/>
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118 <param name="y_ticks_text_size" value="18"/>
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119 </section>
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120 <output_collection name="report" type="list" count="13">
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121 <element file="Isotopologues_cell-Fructose_1,6-bisphosphate.svg" name="Isotopologues_cell-Fructose_1,6-bisphosphate" ftype="svg" compare="sim_size" delta="100"/>
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122 <element file="Isotopologues_cell-L-Aspartic_acid.svg" name="Isotopologues_cell-L-Aspartic_acid" ftype="svg" compare="sim_size" delta="100"/>
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123 <element file="Isotopologues_cell-L-Glutamic_acid.svg" name="Isotopologues_cell-L-Glutamic_acid" ftype="svg" compare="sim_size" delta="100"/>
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124 <element file="Isotopologues_cell-L-Glutamine.svg" name="Isotopologues_cell-L-Glutamine" ftype="svg" compare="sim_size" delta="100"/>
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125 <element file="Isotopologues_cell-L-Lactic_acid.svg" name="Isotopologues_cell-L-Lactic_acid" ftype="svg" compare="sim_size" delta="100"/>
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126 <element file="Isotopologues_cell-L-Lysine.svg" name="Isotopologues_cell-L-Lysine" ftype="svg" compare="sim_size" delta="100"/>
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127 <element file="Isotopologues_cell-L-Proline.svg" name="Isotopologues_cell-L-Proline" ftype="svg" compare="sim_size" delta="100"/>
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128 <element file="Isotopologues_cell-L-Serine.svg" name="Isotopologues_cell-L-Serine" ftype="svg" compare="sim_size" delta="100"/>
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129 <element file="Isotopologues_med-L-Lactic_acid.svg" name="Isotopologues_med-L-Lactic_acid" ftype="svg" compare="sim_size" delta="100"/>
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130 <element file="Isotopologues_med-L-Lysine.svg" name="Isotopologues_med-L-Lysine" ftype="svg" compare="sim_size" delta="100"/>
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131 <element file="Isotopologues_med-L-Proline.svg" name="Isotopologues_med-L-Proline" ftype="svg" compare="sim_size" delta="100"/>
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132 <element file="Isotopologues_med-L-Serine.svg" name="Isotopologues_med-L-Serine" ftype="svg" compare="sim_size" delta="100"/>
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133 <element file="legend_isotopologues_stackedbars.svg" name="legend_isotopologues_stackedbars" ftype="svg" compare="sim_size" delta="100"/>
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134 </output_collection>
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135 </test>
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136 </tests>
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137 <help><![CDATA[
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138 This module is part of DIMet: Differential analysis of Isotope-labeled targeted Metabolomics data (https://pypi.org/project/DIMet/).
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139
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140 DIMet isotopologues plot performs stacked-bars figures for visualization of the isotopologues proportions across all given conditions and all/selected time points, for each metabolite. All the (selected) metabolites are processed automatically.
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141
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142 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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143
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144
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145 **Input data files**
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146
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147 For running DIMet @EXECUTABLE@ you need the following .csv files :
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148
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149 - The **isotopologue proportions** file, and
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150
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151 - 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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152
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153
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154 The isotopologue proportions file must be organized as a matrix:
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155
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156 - The first column must contain isotopologues IDs that are unique (not repeated) within the file.
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157
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158 - The rest of the columns correspond to the samples
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159
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160 - The rows correspond to the isotopologues
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161
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162 - The values must be tab separated, with the first row containing the sample/column labels.
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163
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164
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165
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166 Example - **Isotopologue proportions**:
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167
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168 =============== ================== ================== ================== ================== ================== ==================
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169 ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06**
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170 =============== ================== ================== ================== ================== ================== ==================
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171 2_3-PG_m+0 0.023701408 0.026667837 0.003395407 0.05955 0.034383527 0.12
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172 2_3-PG_m+1 0.0 0.0 0.0 0.0 0.4 0.12
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173 2_3-PG_m+2 0.015379329 0.01506 0.017029723 0.35483229 0.54131313 0.743
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174 2_3-PG_m+3 0.960919263 0.958268099 0.97957487 0.581310816 0.017029723 0.017
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175 2-OHGLu_m+0 0.972778716 0.960016157 0.238843937 0.234383527 0.9998888 0.015064063
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176 2-OHGLu_m+1 0.0 0.0 0.0 0.0 0.0001112 0.960919263
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177 =============== ================== ================== ================== ================== ================== ==================
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178
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179
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180 **Metadata File Information**
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181
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182 Provide a tab-separated file that has the names of the samples in the first column and one header row.
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183 Column names must be exactly in this order:
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184
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185 name_to_plot
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186 condition
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187 timepoint
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188 timenum
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189 compartment
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190 original_name
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191
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192
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193 Example **Metadata File**:
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194
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195
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196 ==================== =============== ============= ============ ================ =================
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197 **name_to_plot** **condition** **timepoint** **timenum** **compartment** **original_name**
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198 -------------------- --------------- ------------- ------------ ---------------- -----------------
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199 Control_cell_T0-1 Control T0 0 cell MCF001089_TD01
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200 Control_cell_T0-2 Control T0 0 cell MCF001089_TD02
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201 Control_cell_T0-3 Control T0 0 cell MCF001089_TD03
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202 Tumoral_cell_T0-1 Tumoral T0 0 cell MCF001089_TD04
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203 Tumoral_cell_T0-2 Tumoral T0 0 cell MCF001089_TD05
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204 Tumoral_cell_T0-3 Tumoral T0 0 cell MCF001089_TD06
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205 Tumoral_cell_T24-1 Tumoral T24 24 cell MCF001089_TD07
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206 Tumoral_cell_T24-2 Tumoral T24 24 cell MCF001089_TD08
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207 Tumoral_cell_T24-3 Tumoral T24 24 cell MCF001090_TD01
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208 Control_med_T24-1 Control T24 24 med MCF001090_TD02
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209 Control_med_T24-2 Control T24 24 med MCF001090_TD03
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210 Tumoral_med_T24-1 Tumoral T24 24 med MCF001090_TD04
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211 Tumoral_med_T24-2 Tumoral T24 24 med MCF001090_TD05
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212 Control_med_T0-1 Control T0 0 med MCF001090_TD06
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213 Tumoral_med_T0-1 Tumoral T0 0 med MCF001090_TD07
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214 Tumoral_med_T0-2 Tumoral T0 0 med MCF001090_TD08
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215 ==================== =============== ============= ============ ================ =================
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216
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217
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218 The column **original_name** must have the names of the samples as given in your data.
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219
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220 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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221 are meaningful is a better choice, as we will take them to display the results.
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222
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223 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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224 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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225
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226 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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227 compartments names are, the longer the output files' names! Please pick short and clear abbreviations to fill this column.
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228
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229
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230 **Running the analysis**
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231
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232
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233 You can precise how you want your analysis to be executed, with the parameters:
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234
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235 - **conditions**: the conditions present in your data, exactly in the ORDER you want them to appear in the x axis of each figure.
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236
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237 - **timepoints**: timepoints to include for the figures.
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238
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239 - **width_each_stack** : the desired width (in inches) for the the individual metabolite figure.
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240
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241 - **inner_numbers_size**: by default, the arithmetic mean over the biological replicates for a given isotopologue is displayed in the middle of each bar portion, the default font size is 13.5. Set to 0 if you do not want to show these values.
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242
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243 There exist hints on use that will guide you, next to the parameters.
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244
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245 The output consist of stacked-bar figures, one by each metabolite, and one legend .pdf file, common to all the produced figures.
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246
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247 **Available data for testing**
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248
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249 You can test our tool with the data from our manuscript https://zenodo.org/record/10579862 (the pertinent
0
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250 files for you are located in the subfolders inside the data folder).
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251 You can also use the minimal data examples from https://zenodo.org/record/10579891
0
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252
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253 ]]>
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254 </help>
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255 <expand macro="citations"/>
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256 </tool>