--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/boxplot.xml	Mon Apr 04 10:29:47 2022 +0000
@@ -0,0 +1,123 @@
+<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
+                ## detailed_output = TRUE
+            )
+            @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="total">Total</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"/>
+        </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="total"/>
+            <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"/>
+        </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"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+What it does
+============
+
+Generates boxplots of the most abundant taxa.
+
+The Galaxy tool calls the `amp_boxplot
+<https://madsalbertsen.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>
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