Mercurial > repos > iuc > dimet_abundance_plot
diff dimet_abundance_plot.xml @ 0:c9040bdb918c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
| author | iuc |
|---|---|
| date | Tue, 10 Oct 2023 11:55:25 +0000 |
| parents | |
| children | 07164270ec13 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dimet_abundance_plot.xml Tue Oct 10 11:55:25 2023 +0000 @@ -0,0 +1,233 @@ +<tool id="dimet_@EXECUTABLE@" name="dimet @TOOL_LABEL@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> + <description> + Figures of metabolites total abundance as barplots (by DIMet) + </description> + <macros> + <token name="@TOOL_LABEL@">abundance plot</token> + <token name="@EXECUTABLE@">abundance_plot</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + @INIT_CONFIG@ + @INIT_ABUNDANCE_PLOT@ + @INIT_CONDITIONS@ + @INIT_TIMEPOINTS@ + @INIT_ENRICHMENT_METABOLITES@ + HYDRA_FULL_ERROR=1 python -m dimet + -cp '$__new_file_path__/config' + '++hydra.run.dir=abundance_plot' + '++figure_path=figures' + '++table_path=tables' + '++analysis={ + metabolites:${metabolites}, + dataset:{ + _target_:dimet.data.DatasetConfig, + name: "Galaxy DIMet run" + }, + method:{ + _target_: dimet.method.AbundancePlotConfig, + label: abundance_plot, + name: "Generate abundance plots", + barcolor: timepoint, + axisx: condition, + axisx_labeltilt: '${output_options.axisx_labeltilt}', + height_each_subfig: '${output_options.height_each_subfig}', + palette:${output_options.palette}, + as_grid:${output_options.as_grid}, + do_stripplot:${output_options.do_stripplot}, + figure_format:${output_options.figure_format} + }, + label: abundance_plot, + width_each_subfig: '${output_options.width_each_subfig}' + }' + '++analysis.dataset.label=' + '++analysis.timepoints=${timepoints}' + '++analysis.dataset.subfolder=' + '++analysis.dataset.conditions=${conds}' + #if $metadata_path: + '++analysis.dataset.metadata=metadata' + #end if + #if $abundance_file: + '++analysis.dataset.abundances=abundance' + #end if + @REMOVE_CONFIG@ + ]]></command> + <inputs> + <expand macro="input_parameters_abundance"/>xz + <expand macro="conditions"/> + <expand macro="timepoint"/> + <expand macro="compartments_abundance"/> + <expand macro="abundance_metabolites_list"/> + <section name="output_options" title="Output options"> + <param name="palette" type="select" value="pastel" display="radio" label="Select palette colormap to apply to abundance plot" help="Please enter at max 1 statistical test by file"> + <option value="pastel">pastel</option> + <option value="Set1">Set1</option> + <option value="Set2">Set2</option> + <option value="Set3">Set3</option> + <option value="Dark2">Dark2</option> + </param> + <param name="figure_format" type="select" value="pdf" display="radio" label="Select output figure format" help="Please enter at max 1 format"> + <option value="pdf">Pdf</option> + <option value="svg">Svg</option> + </param> + <param name="axisx_labeltilt" type="integer" min="0" max="180" value="70" label="X axis label tilt" + help="Default value is 70."/> + <param name="width_each_subfig" type="float" min="1.0" max="15.0" value="3.0" label="width of subfig plots" + help="Default value is 3."/> + <param name="height_each_subfig" type="float" min="1.0" max="15.0" value="5.5" label="height of subfig plots" + help="Default value is 5.5"/> + <param name="as_grid" type="boolean" value="false" label="plot as grid" + help="Default value is false."/> + <param name="do_stripplot" type="boolean" value="false" label="add strip plot on abundance bar" + help="Default value is false."/> + + </section> + </inputs> + <outputs> + <collection name="report" type="list"> + <discover_datasets pattern="__designation_and_ext__" directory="figures"/> + </collection> + </outputs> + <tests> + <test> + <param name="abundance_file" ftype="tabular" value="AbundanceCorrected.csv"/> + <param name="metadata_path" ftype="tabular" value="example1_metadata.csv"/> + <param name="conditions" value='sgLDHA'/> + <param name="timepoint" value='T0,T24'/> + <param name="compartments" value='endo'/> + <param name="metabolites_list" value="Fru1P"/> + <section name="output_options"> + <param name="axisx_labeltilt" value="70"/> + <param name="palette" value="pastel"/> + <param name="width_each_subfig" value="3.0"/> + <param name="height_each_subfig" value="5.5"/> + <param name="as_grid" value="false"/> + <param name="do_stripplot" value="false"/> + <param name="figure_format" value="svg"/> + </section> + <output_collection name="report" type="list" count="2"> + <element file="bars_endo_Fru1P-total_abundance.svg" name="bars_endo_Fru1P-total_abundance" ftype="svg" compare="sim_size" delta="100"/> + <element file="legend.svg" name="legend" ftype="svg" compare="sim_size" delta="100"/> + </output_collection> + </test> + </tests> + <help><![CDATA[ + +This module is part of DIMet: Differential analysis of Isotope-labeled targeted Metabolomics data (https://pypi.org/project/DIMet/). + +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. + +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. + + + **Input data files** + +For running DIMet @EXECUTABLE@ you need the following .csv files : + +- The total **abundances** file, and + +- The metadata file, a unique file with the description of the samples. This file is compulsory (see section **Metadata File Information**). + + +The total abundances file must be organized as a matrix: +- The first column must contain Metabolite IDs that are unique (not repeated) within the file. +- The rest of the columns correspond to the samples +- The rows correspond to the metabolites +- The values must be tab separated, with the first row containing the sample/column labels. + + + +Example - Metabolites **abundances**: + + =============== ================== ================== ================== ================== ================== ================== + ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06** + =============== ================== ================== ================== ================== ================== ================== + 2_3-PG 8698823.9926 10718737.7217 10724373.9 8536484.5 22060650 28898956 + 2-OHGLu 36924336 424336 92060650 45165 84951950 965165051 + Glc6P 2310 2142 2683 1683 012532068 1252172 + Gly3P 399298 991656565 525195 6365231 89451625 4952651963 + IsoCit 0 0 0 84915613 856236 954651610 + =============== ================== ================== ================== ================== ================== ================== + + +**Metadata File Information** + +Provide a tab-separated file that has the names of the samples in the first column and one header row. +Column names must be exactly in this order: + + name_to_plot + condition + timepoint + timenum + compartment + original_name + + +Example **Metadata File**: + + + ==================== =============== ============= ============ ================ ================= + **name_to_plot** **condition** **timepoint** **timenum** **compartment** **original_name** + -------------------- --------------- ------------- ------------ ---------------- ----------------- + Control_cell_T0-1 Control T0 0 cell MCF001089_TD01 + Control_cell_T0-2 Control T0 0 cell MCF001089_TD02 + Control_cell_T0-3 Control T0 0 cell MCF001089_TD03 + Tumoral_cell_T0-1 Tumoral T0 0 cell MCF001089_TD04 + Tumoral_cell_T0-2 Tumoral T0 0 cell MCF001089_TD05 + Tumoral_cell_T0-3 Tumoral T0 0 cell MCF001089_TD06 + Tumoral_cell_T24-1 Tumoral T24 24 cell MCF001089_TD07 + Tumoral_cell_T24-2 Tumoral T24 24 cell MCF001089_TD08 + Tumoral_cell_T24-3 Tumoral T24 24 cell MCF001090_TD01 + Control_med_T24-1 Control T24 24 med MCF001090_TD02 + Control_med_T24-2 Control T24 24 med MCF001090_TD03 + Tumoral_med_T24-1 Tumoral T24 24 med MCF001090_TD04 + Tumoral_med_T24-2 Tumoral T24 24 med MCF001090_TD05 + Control_med_T0-1 Control T0 0 med MCF001090_TD06 + Tumoral_med_T0-1 Tumoral T0 0 med MCF001090_TD07 + Tumoral_med_T0-2 Tumoral T0 0 med MCF001090_TD08 + ==================== =============== ============= ============ ================ ================= + + +The column **original_name** must have the names of the samples as given in your data. + +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 +are meaningful is a better choice, as we will take them to display the results. + +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) +nor any other symbol). Make sure these time numbers are in the same units (but do not write the units here!). + +The column **compartment** is an abbreviation, coined by you, for the compartments. This will be used for the results' files names: the longer the +compartments names are, the longer the output files' names! Please pick short and clear abbreviations to fill this column. + + +**Running the analysis** + + +You can precise how you want your analysis to be executed, with the parameters: + +- **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. + +- **timepoints** : the selected (you can select all) time points, that will be shown in the x axis. + +- **width_each_subfig** : the desired width (in inches) for the the individual metabolites' figures + + + +There exist hints on use that will guide you, next to the parameters. + + +The output consists of bar-plot figures, one by each metabolite, and one legend .pdf file, common to all the produced figures. + + + +**Available data for testing** + +You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent +files for you are located in the subfolders inside the data folder). +Tou can also use the minimal data examples from https://zenodo.org/record/8380706 + + ]]> + </help> + <expand macro="citations"/> +</tool> \ No newline at end of file