Mercurial > repos > iuc > dimet_abundance_plot

annotate dimet_abundance_plot.xml @ 7:4b4dead87318 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 17:39:02 +0000
parents db1e58e44a5c
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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 metabolites total abundance as barplots (by DIMet)
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4 </description>
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5 <macros>
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6 <token name="@TOOL_LABEL@">abundance plot</token>
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7 <token name="@EXECUTABLE@">abundance_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_ABUNDANCE_PLOT@
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14 @INIT_ABUNDANCE_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
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18 '++hydra.run.dir=.'
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19 '++figure_path=figures'
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20 '++table_path=tables'
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21 '++analysis={
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22 metabolites:${metabolites},
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23 dataset:{
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24 _target_:dimet.data.DatasetConfig,
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25 name: "Galaxy DIMet run"
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26 },
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27 method:{
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28 _target_: dimet.method.AbundancePlotConfig,
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29 label: abundance_plot,
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30 name: "Generate abundance plots",
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31 barcolor: '${output_options.bar_color}',
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32 axisx: ${axisx},
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33 axisx_labeltilt: '${output_options.axisx_labeltilt}',
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34 height_each_subfig: '${output_options.height_each_subfig}',
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35 palette:${output_options.palette},
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36 as_grid:${output_options.as_grid},
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37 x_text_modify_as:null,
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38 do_stripplot:${output_options.do_stripplot},
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39 figure_format:${output_options.figure_format}
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40 },
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41 label: abundance_plot,
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42 width_each_subfig: '${output_options.width_each_subfig}'
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43 }'
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44 '++analysis.dataset.label='
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45 '++analysis.timepoints=${timepoints}'
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46 '++analysis.dataset.subfolder='
2
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47 '++analysis.dataset.conditions=${conditions}'
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48 #if $metadata_path:
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49 '++analysis.dataset.metadata=metadata'
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50 #end if
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51 #if $abundance_file:
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52 '++analysis.dataset.abundances=abundance'
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53 #end if
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54 @REMOVE_CONFIG@
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55 ]]></command>
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56 <inputs>
1
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57 <expand macro="input_parameters_abundance"/>
2
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58 <expand macro="plot_abundance_factor_list"/>
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59 <expand macro="timepoint"/>
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60 <expand macro="compartments_abundance"/>
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61 <expand macro="abundance_metabolites_list"/>
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62 <section name="output_options" title="Output options">
2
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63 <expand macro="palette"/>
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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>
5
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68 <param name="bar_color" type="select" value="timepoint" display="radio" label="Select output figure barcolor" help="Please enter at max 1 format">
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69 <option value="timepoint">timepoint</option>
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70 <option value="condition">condition</option>
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71 </param>
0
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72 <param name="axisx_labeltilt" type="integer" min="0" max="180" value="70" label="X axis label tilt"
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73 help="Default value is 70."/>
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74 <param name="width_each_subfig" type="float" min="1.0" max="15.0" value="3.0" label="width of subfig plots"
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75 help="Default value is 3."/>
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76 <param name="height_each_subfig" type="float" min="1.0" max="15.0" value="5.5" label="height of subfig plots"
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77 help="Default value is 5.5"/>
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78 <param name="as_grid" type="boolean" value="false" label="plot as grid"
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79 help="Default value is false."/>
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80 <param name="do_stripplot" type="boolean" value="false" label="add strip plot on abundance bar"
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81 help="Default value is false."/>
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82 </section>
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83 </inputs>
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84 <outputs>
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85 <collection name="report" type="list">
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86 <discover_datasets pattern="__designation_and_ext__" directory="figures"/>
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87 </collection>
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88 </outputs>
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89 <tests>
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90 <test>
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91 <param name="abundance_file" ftype="tabular" value="AbundanceCorrected.csv"/>
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92 <param name="metadata_path" ftype="tabular" value="example1_metadata.csv"/>
2
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93 <repeat name="plot_abundance_factor_list">
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94 <param name="condition" value="sgLDHA"/>
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95 </repeat>
0
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96 <param name="timepoint" value='T0,T24'/>
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97 <param name="compartments" value='endo'/>
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98 <param name="metabolites_list" value="Fru1P"/>
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99 <section name="output_options">
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100 <param name="axisx_labeltilt" value="70"/>
5
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101 <param name="bar_color" value="timepoint"/>
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102 <param name="axisx" value="condition"/>
0
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103 <param name="palette" value="pastel"/>
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104 <param name="width_each_subfig" value="3.0"/>
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105 <param name="height_each_subfig" value="5.5"/>
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106 <param name="as_grid" value="false"/>
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107 <param name="do_stripplot" value="false"/>
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108 <param name="figure_format" value="svg"/>
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109 </section>
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110 <output_collection name="report" type="list" count="2">
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111 <element file="bars_endo_Fru1P-total_abundance.svg" name="bars_endo_Fru1P-total_abundance" ftype="svg" compare="sim_size" delta="100"/>
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112 <element file="legend.svg" name="legend" ftype="svg" compare="sim_size" delta="100"/>
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113 </output_collection>
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114 </test>
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115 </tests>
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116 <help><![CDATA[
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117
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118 This module is part of DIMet: Differential analysis of Isotope-labeled targeted Metabolomics data (https://pypi.org/project/DIMet/).
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119
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120 DIMet total abundances plot performs comparative bars for visualization of the total abundances of each metabolite across the different conditions present in your data and all/selected time points. All (or selected) metabolites are processed automatically.
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121
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122 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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123
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124
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125 **Input data files**
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126
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127 For running DIMet @EXECUTABLE@ you need the following .csv files :
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128
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129 - The total **abundances** file, and
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130
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131 - 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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132
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133
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134 The total abundances file must be organized as a matrix:
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135 - The first column must contain Metabolite IDs that are unique (not repeated) within the file.
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136 - The rest of the columns correspond to the samples
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137 - The rows correspond to the metabolites
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138 - The values must be tab separated, with the first row containing the sample/column labels.
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139
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140
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141
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142 Example - Metabolites **abundances**:
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143
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144 =============== ================== ================== ================== ================== ================== ==================
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145 ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06**
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146 =============== ================== ================== ================== ================== ================== ==================
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147 2_3-PG 8698823.9926 10718737.7217 10724373.9 8536484.5 22060650 28898956
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148 2-OHGLu 36924336 424336 92060650 45165 84951950 965165051
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149 Glc6P 2310 2142 2683 1683 012532068 1252172
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150 Gly3P 399298 991656565 525195 6365231 89451625 4952651963
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151 IsoCit 0 0 0 84915613 856236 954651610
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152 =============== ================== ================== ================== ================== ================== ==================
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153
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154
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155 **Metadata File Information**
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156
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157 Provide a tab-separated file that has the names of the samples in the first column and one header row.
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158 Column names must be exactly in this order:
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159
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160 name_to_plot
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161 condition
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162 timepoint
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163 timenum
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164 compartment
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165 original_name
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166
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167
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168 Example **Metadata File**:
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169
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170
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171 ==================== =============== ============= ============ ================ =================
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172 **name_to_plot** **condition** **timepoint** **timenum** **compartment** **original_name**
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173 -------------------- --------------- ------------- ------------ ---------------- -----------------
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174 Control_cell_T0-1 Control T0 0 cell MCF001089_TD01
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175 Control_cell_T0-2 Control T0 0 cell MCF001089_TD02
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176 Control_cell_T0-3 Control T0 0 cell MCF001089_TD03
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177 Tumoral_cell_T0-1 Tumoral T0 0 cell MCF001089_TD04
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178 Tumoral_cell_T0-2 Tumoral T0 0 cell MCF001089_TD05
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179 Tumoral_cell_T0-3 Tumoral T0 0 cell MCF001089_TD06
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180 Tumoral_cell_T24-1 Tumoral T24 24 cell MCF001089_TD07
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181 Tumoral_cell_T24-2 Tumoral T24 24 cell MCF001089_TD08
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182 Tumoral_cell_T24-3 Tumoral T24 24 cell MCF001090_TD01
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183 Control_med_T24-1 Control T24 24 med MCF001090_TD02
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184 Control_med_T24-2 Control T24 24 med MCF001090_TD03
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185 Tumoral_med_T24-1 Tumoral T24 24 med MCF001090_TD04
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186 Tumoral_med_T24-2 Tumoral T24 24 med MCF001090_TD05
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187 Control_med_T0-1 Control T0 0 med MCF001090_TD06
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188 Tumoral_med_T0-1 Tumoral T0 0 med MCF001090_TD07
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189 Tumoral_med_T0-2 Tumoral T0 0 med MCF001090_TD08
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190 ==================== =============== ============= ============ ================ =================
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191
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192
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193 The column **original_name** must have the names of the samples as given in your data.
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194
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195 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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196 are meaningful is a better choice, as we will take them to display the results.
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197
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198 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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199 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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200
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201 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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202 compartments names are, the longer the output files' names! Please pick short and clear abbreviations to fill this column.
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203
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204
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205 **Running the analysis**
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206
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207
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208 You can precise how you want your analysis to be executed, with the parameters:
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209
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210 - **conditions** : the conditions present in your data, exactly in the ORDER you want them to appear both in the x axis and in the legend.
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211
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212 - **timepoints** : the selected (you can select all) time points, that will be shown in the x axis.
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213
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214 - **width_each_subfig** : the desired width (in inches) for the the individual metabolites' figures
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215
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216
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217
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218 There exist hints on use that will guide you, next to the parameters.
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219
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220
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221 The output consists of bar-plot figures, one by each metabolite, and one legend .pdf file, common to all the produced figures.
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222
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223
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224
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225 **Available data for testing**
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226
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227 You can test our tool with the data from our manuscript https://zenodo.org/record/10579862 (the pertinent
0
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228 files for you are located in the subfolders inside the data folder).
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229 You can also use the minimal data examples from https://zenodo.org/record/10579891
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230
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231 ]]>
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232 </help>
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233 <expand macro="citations"/>
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234 </tool>