Mercurial > repos > artbio > ez_histograms
diff ez_histograms.xml @ 0:bdf40b0924cb draft
planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
author | artbio |
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date | Wed, 07 Feb 2024 19:49:56 +0000 |
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children | fbedb212982d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ez_histograms.xml Wed Feb 07 19:49:56 2024 +0000 @@ -0,0 +1,166 @@ +<tool id="ez_histograms" name="ez_histograms" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <macros> + <token name="@TOOL_VERSION@">3.4.4</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">23.0</token> + </macros> + <requirements> + <requirement type="package" version="3.4.4">r-ggplot2</requirement> + <requirement type="package" version="1.4.4">r-reshape2</requirement> + <requirement type="package" version="1.1.4">r-dplyr</requirement> + <requirement type="package" version="1.3.0">r-scales</requirement> + <requirement type="package" version="1.4.6">r-vtable</requirement> + <requirement type="package" version="1.7.4">r-optparse</requirement> + </requirements> + + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + + <command detect_errors="exit_code"><![CDATA[ + Rscript $__tool_directory__/ez_histograms.R + --file '$file' + --profile '$plot_options.plot_options_selector' + --xscale '$plot_options.xscale' + #if str($plot_options.plot_options_selector) == "count": + --yscale '$plot_options.yscale' + #end if + --pdf '$pdf' + --summary '$summary' + ]]></command> + + <inputs> + <param name="file" type="data" format="tabular" label="Input tabular dataset" + help="Only numeric columns will be plotted"/> + <conditional name="plot_options"> + <param name="plot_options_selector" type="select" label="Set plot types"> + <option value="count" selected="true">Count Histograms</option> + <option value="density">Density Plots</option> + </param> + <when value="density"> + <param name="xscale" type="select" label="Set x-axis scale"> + <option value="cartesian" selected="true">Cartesian</option> + <option value="log2">log2</option> + <option value="log10">log10</option> + </param> + </when> + <when value="count"> + <param name="xscale" type="select" label="Set x-axis scale"> + <option value="cartesian" selected="true">Cartesian</option> + <option value="log2">log2</option> + <option value="log10">log10</option> + </param> + <param name="yscale" type="select" label="Set y-axis scale"> + <option value="cartesian" selected="true">Cartesian</option> + <option value="log2">log2</option> + <option value="log10">log10</option> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data name="pdf" format="pdf" label="${tool.name} plots from ${on_string}"/> + <data name="summary" format="tabular" label="Statistics Summary from ${on_string}"/> + </outputs> + <tests> + <test expect_num_outputs="2"> + <param name="file" value="classic.tsv"/> + <param name="plot_options_selector" value="count"/> + <param name="xscale" value="cartesian"/> + <param name="yscale" value="cartesian"/> + <output name="pdf" file="classic.pdf"/> + <output name="summary" file="summary_1.tsv"/> + </test> + <test expect_num_outputs="2"> + <param name="file" value="counts.tsv"/> + <param name="plot_options_selector" value="count"/> + <param name="xscale" value="log2"/> + <param name="yscale" value="cartesian"/> + <output name="pdf" file="count.pdf"/> + <output name="summary" file="summary_2.tsv"/> + </test> + <test expect_num_outputs="2"> + <param name="file" value="headless.tsv"/> + <param name="plot_options_selector" value="count"/> + <param name="xscale" value="log10"/> + <param name="yscale" value="log2"/> + <output name="pdf" file="headless.pdf"/> + <output name="summary" file="summary_3.tsv"/> + </test> + <test expect_num_outputs="2"> + <param name="file" value="large.tsv"/> + <param name="plot_options_selector" value="density"/> + <param name="xscale" value="log2"/> + <output name="pdf" file="large.pdf"/> + <output name="summary" file="summary_4.tsv"/> + </test> + <test expect_num_outputs="2"> + <param name="file" value="rowheadless.tsv"/> + <param name="plot_options_selector" value="density"/> + <param name="xscale" value="cartesian"/> + <output name="pdf" file="rowheadless.pdf"/> + <output name="summary" file="summary_5.tsv"/> + </test> + <test expect_num_outputs="2"> + <param name="file" value="single_headed_col.tsv"/> + <param name="plot_options_selector" value="density"/> + <param name="xscale" value="log10"/> + <output name="pdf" file="single_headed_col.pdf"/> + <output name="summary" file="summary_6.tsv"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +The tool generates faceted histograms or density plots using the ggplot2 functions +geom_histogram() or geom_density(), respectively. + +**Inputs** + +Any regular tabular data, provided that the number of columns (tabulations) is unchanged +for any row. + +Except for the first one, any column will be considered as one variable with n_rows +observations. However, non-numeric columns will be filtered and will not be considered +variables. + +If the first column is not numeric, it will be taken as row names (ie observation identifiers), +otherwise, it will be considered as the first numerical variable of the table. + +If the first row is not numerical, it will be considered as a header, ie as describing the +variable names. + +If you provide a table without header, variable names will be assigned to each column +following the R default rule: (V1), V2, ..., Vn + +**Parameters** + +For Count Histograms, both x- and y-axis can have linear (cartesian), log2 or log10 scales. + +For Density Plots, only x-axis can be customized with linear (cartesian), log2, or log10 +scales + +**Outputs** + +The ez_histograms Galaxy tool returns + +- A pdf file with plots faceted on three columns +- A tsv file with statistics summary of the variables generated by the R package vtables + + ]]></help> + <citations> + <citation type="bibtex"> +@BOOK{Wickham2016-ic, + title = "Ggplot2: Elegant graphics for data analysis", + author = "Wickham, Hadley", + publisher = "Springer International Publishing", + series = "Use R!", + edition = 2, + month = jun, + year = 2016, + address = "Cham, Switzerland", + language = "en", + isbn = "9783319242774" +} </citation> + </citations> +</tool>