Mercurial > repos > iuc > ampvis2_boxplot
view boxplot.xml @ 4:b4c6f8741989 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit ab75ba7665d7fb5c18ad08dfbba92b273f991dfc
author | iuc |
---|---|
date | Sat, 16 Mar 2024 11:39:04 +0000 |
parents | 6eae290d762b |
children |
line wrap: on
line source
<tool id="ampvis2_boxplot" name="ampvis2 boxplot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> <description></description> <macros> <import>macros.xml</import> </macros> <expand macro="header"/> <command detect_errors="exit_code"><![CDATA[ Rscript '$rscript' ]]></command> <configfiles> <configfile name="rscript"><![CDATA[ #if $tax_add #set ta='c("' + '", "'.join(str($tax_add).split(",")) + '")' #else #set ta='NULL' #end if library(ampvis2, quietly = TRUE) d <- readRDS("$data") plot <- amp_boxplot( d, #if $group_by group_by = "$group_by", #end if sort_by = "$sort_by", plot_type = "$plot_type", point_size = $point_size, tax_aggregate = "$tax_aggregate", tax_add = $ta, @TAX_SHOW@ tax_empty = "$tax_empty", ## tax_class = NULL, ## order_group = NULL, ## order_y = NULL, plot_flip = $plot_flip, plot_log = $plot_log, #if str($adjust_zero) != "" adjust_zero = $adjust_zero, #end if normalise = $normalise ) @OUTPUT_TOKEN@ ]]></configfile> </configfiles> <inputs> <expand macro="rds_metadata_input_macro"/> <expand macro="metadata_select_discrete" argument="group_by" label="Group the samples" help="by a discrete variable in the metadata"/> <param argument="sort_by" type="select" label="Sort boxplots by"> <option value="median">Median</option> <option value="mean">Mean</option> <option value="sum">Sum</option> </param> <param argument="plot_type" type="select" label="Plot type"> <option value="boxplot">Boxplot</option> <option value="point">Points</option> </param> <param argument="point_size" type="integer" value="1" min="0" label="Point size"/> <expand macro="taxlevel_macro" argument="tax_aggregate" label="The taxonomic level to aggregate the OTUs"> <option value="Genus" selected="true">Genus</option> </expand> <expand macro="taxlevel_macro" argument="tax_add" multiple="true" optional="true" label="Additional taxonomic level(s) to display"/> <expand macro="tax_show_macro" value="20"/> <expand macro="tax_empty_macro"/> <param argument="plot_flip" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Flip the axes of the plot"/> <param argument="plot_log" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Log10-scale the plot"/> <param argument="adjust_zero" type="integer" value="" min="1" optional="true" label="Add value to abundances" help="in order to keep abundances of 0 in the calculation of medians"/> <expand macro="normalise_macro"/> <expand macro="out_format_macro"/> </inputs> <outputs> <expand macro="out_macro"/> </outputs> <tests> <test> <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> <output name="plot" value="AalborgWWTPs-boxplot.pdf" ftype="pdf" compare="sim_size"/> </test> <test> <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> <param name="group_by" value="Plant"/> <param name="sort_by" value="sum"/> <param name="tax_show" value="5"/> <param name="plot_flip" value="true"/> <param name="plot_log" value="true"/> <param name="adjust_zero" value="100000"/> <param name="normalise" value="true"/> <output name="plot" value="AalborgWWTPs-boxplot-group.pdf" ftype="pdf" compare="sim_size"/> </test> <test> <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> <param name="plot_type" value="point"/> <param name="point_size" value="5"/> <param name="tax_aggregate" value="Order"/> <param name="tax_add" value="Phylum"/> <output name="plot" value="AalborgWWTPs-boxplot-point.pdf" ftype="pdf" compare="sim_size"/> </test> </tests> <help><![CDATA[ What it does ============ Generates boxplots of the most abundant taxa. The Galaxy tool calls the `amp_boxplot <https://kasperskytte.github.io/ampvis2/reference/amp_boxplot.html>`_ function of the ampvis2 package. Input ===== @HELP_RDS_INPUT@ @HELP_METADATA_LIST_INPUT@ Output ====== Boxplot in the chosen output format. ]]></help> <expand macro="citations"/> </tool>