--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/heatmap.xml	Mon Apr 04 10:21:36 2022 +0000
@@ -0,0 +1,337 @@
+<tool id="ampvis2_heatmap" name="ampvis2 heatmap" 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")
+            #if $output_options.out_format == "tabular"
+                raw <-
+            #else
+                plot <-
+            #end if
+            amp_heatmap(
+                d
+                ,
+                #if $group_by
+                    group_by = "$group_by",
+                #end if
+                #if $facet_by
+                    facet_by = "$facet_by",
+                #end if
+                normalise = $normalise,
+                tax_aggregate = "$tax_aggregate",
+                tax_add = $ta,
+                @TAX_SHOW@
+                showRemainingTaxa = $showRemainingTaxa,
+                ## tax_class = NULL,
+                tax_empty = "$tax_empty",
+                ## TODO giving the order of the columns is difficult but "cluster" would be nice I guess
+                ## order_x_by = NULL,
+                ## order_y_by = NULL,
+                plot_values = $plot_values_cond.plot_values,
+                #if $plot_values_cond.plot_values == "TRUE"
+                    plot_values_size = $plot_values_cond.plot_values_size,
+                #end if
+                ## plot_legendbreaks = NULL,
+                plot_colorscale = "$plot_colorscale",
+                plot_na = $plot_na,
+                measure = "$measure",
+                #if str($min_abundance) != ''
+                    min_abundance = $min_abundance,
+                #end if
+                #if str($max_abundance) != ''
+                    max_abundance = $max_abundance,
+                #end if
+                #if $sort_by_cond.sort_by_sel != 'no'
+                    sort_by = "$sort_by_cond.sort_by",
+                #end if
+                ## TODO https://github.com/MadsAlbertsen/ampvis2/issues/130
+                ## #if $normalise_by_cond.normalise_by_sel != "no"
+                ##     normalise_by = "$normalise_by_cond.normalise_by",
+                ## #end if
+                #if $scale_by
+                    scale_by = "$scale_by",
+                #end if
+                ## color_vector = NULL
+                ## round = 1,
+                #if $output_options.out_format == "tabular"
+                    textmap = TRUE,
+                #else
+                    textmap = FALSE,
+                #end if
+                #if $plot_functions_cond.plot_functions_sel != "no"
+                    plot_functions = TRUE,
+                    #if $plot_functions_cond.plot_functions_sel == "file"
+                        function_data = read.table("$plot_functions_cond.function_data", header = TRUE, sep = "\t"),
+                    #end if
+                    #set foo='c("' + '", "'.join(str($plot_functions_cond.functions).split(",")) + '")'
+                    functions = $foo,
+                #end if
+                rel_widths = c(0.75, 0.25) 
+            )
+            #if $output_options.out_format != "tabular"
+                @OUTPUT_TOKEN@
+            #else
+                write.table(raw, file = "$plot_raw", sep = "\t") 
+            #end if
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="rds_metadata_input_macro"/>
+        <expand macro="metadata_select_discrete" argument="group_by" label="Group samples" help="By a categorical variable in the metadata"/>
+        <expand macro="metadata_select_discrete" argument="facet_by" label="Facet the samples" help="By a categorical variable in the metadata."/>
+        <expand macro="normalise_macro" checked="true"/>
+        <expand macro="taxlevel_macro" argument="tax_aggregate" label="The taxonomic level to aggregate the OTUs">
+            <option value="Phylum" selected="true">Phylum</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="10"/>
+        <param argument="showRemainingTaxa" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Display sum of remaining taxa" help="Add an additional row at the bottom displaying the sum of all remaining taxa that are not part of the top tax_show most abundant taxa."/>
+        <expand macro="tax_empty_macro"/>
+        <conditional name="plot_values_cond">
+            <param argument="plot_values" type="select" label="Plot the values on the heatmap">
+                <option value="TRUE">Yes</option>
+                <option value="FALSE">No</option>
+            </param>
+            <when value="TRUE">
+                <param name="plot_values_size" type="integer" value="4" label="Size of the plotted values"/>
+            </when>
+            <when value="FALSE"/>
+        </conditional>
+        <param argument="plot_colorscale" type="select" label="Type of scale used for coloring abundances">
+            <option value="sqrt">Square root (sqrt)</option>
+            <option value="log10" selected="true">Log (log10)</option>
+        </param>
+        <param argument="plot_na" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Color missing values with the lowest color in the scale"/>
+        <param argument="measure" type="select" label="Value to show across the groups">
+            <option value="mean">Mean</option>
+            <option value="max">Maximum</option>
+            <option value="median">Median</option>
+        </param>
+        <param argument="min_abundance" type="float" value="0.1" min="0" optional="true" label="Maximum abundance" help="All values below this value are given the same color."/>
+        <param argument="max_abundance" type="float" value="" min="0" optional="true" label="Maximum abundance" help="All values above this value are given the same color." />
+
+        <conditional name="sort_by_cond">
+            <param name="sort_by_sel" type="select" label="Sort heatmap by most abundant taxa">
+                <option value="no">No</option>
+                <option value="group">in a group of samples</option>
+                <option value="sample">in a specific sample</option>
+            </param>
+            <when value="no"/>
+            <when value="group">
+                <param argument="sort_by" type="select" optional="true" label="Group to sort by">
+                    <options from_dataset="metadata_list">
+                        <column name="name" index="1"/>
+                        <column name="value" index="1"/>
+                        <filter type="param_value" column="0" ref="group_by"/>
+                        <filter type="unique_value" column="1"/>
+                    </options>
+                </param>
+            </when>
+            <when value="sample">
+                <param argument="sort_by" type="select" optional="true" label="Sample to sort by">
+                    <options from_dataset="metadata_list">
+                        <column name="name" index="1"/>
+                        <column name="value" index="1"/>
+                        <filter type="static_value" value="TRUE" column="2"/> <!-- filter samples -->
+                        <filter type="unique_value" column="1"/>
+                    </options>
+                </param>
+            </when>
+        </conditional>
+        <!-- TODO https://github.com/MadsAlbertsen/ampvis2/issues/130  -->
+        <!-- <expand macro="metadata_sample_select" argument="normalise_by" label="Normalize counts by a variable or a specific sample"/> -->
+        <expand macro="metadata_select_discrete" argument="scale_by" label="Scale the abundances by a variable in the metadata"/>
+
+        <conditional name="plot_functions_cond">
+            <param name="plot_functions_sel" type="select" label="Show functional information about the Genus-level OTUs" help="Produces a 2-column grid plot, showing known functional information about the Genus-level OTUs next to the heatmap. When using this feature, make sure that either tax_aggregate or tax_add is set to Genus and that Genus is the lowest level in either.">
+                <option value="no">No</option>
+                <option value="midasfieldguide">Use data from midasfieldguide.org</option>
+                <option value="file">Use data from a dataset in the history</option>
+            </param>
+            <when value="no"/>
+            <when value="file">
+                <!-- neeed tsv here since tabular does not fill the column_names
+                     metadata and therefore the data_meta filter in the functions
+                     select would not work-->
+                <param argument="function_data" type="data" format="tsv" label="Tabular dataset with functional information at Genus level" help="See help"/>
+                <param argument="functions" type="select" multiple="true" label="Function(s) to include">
+                    <options>
+                        <filter type="data_meta" ref="function_data" key="column_names"/>
+                        <filter type="remove_value" value="Genus"/>
+                    </options>
+                </param>
+            </when>
+            <when value="midasfieldguide">
+                <param name="functions" type="select" multiple="true" label="Function(s) to include">
+                    <option value="MiDAS" selected="true">MiDAS</option>
+                    <option value="Filamentous" selected="true">Filamentous</option>
+                    <option value="AOB" selected="true">AOB</option>
+                    <option value="NOB" selected="true">PAO</option>
+                    <option value="GAO" selected="true">GAO</option>
+                </param>
+            </when>
+        </conditional>
+        <expand macro="out_format_macro">
+            <option value="tabular">Table</option>
+        </expand>
+    </inputs>
+    <outputs>
+        <expand macro="out_macro">
+            <filter>output_options["out_format"] != "tabular"</filter>
+        </expand>
+        <data name="plot_raw" format="tabular">
+            <filter>output_options["out_format"] == "tabular"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- defaults -->
+        <test expect_num_outputs="1">
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
+            <output name="plot" value="AalborgWWTPs-heatmap.pdf" ftype="pdf"/>
+        </test>
+        <!-- group and facet-->
+        <test expect_num_outputs="1">
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
+            <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 
+            <param name="group_by" value="Plant"/>
+            <param name="facet_by" value="Year"/>
+            <output name="plot_raw" value="AalborgWWTPs-heatmap-group-facet.pdf" ftype="pdf"/>
+        </test>
+        <!-- group and facet and test raw output -->
+        <test expect_num_outputs="1">
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
+            <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 
+            <param name="group_by" value="Plant"/>
+            <param name="facet_by" value="Year"/>
+            <param name="out_format" value="tabular"/>
+            <output name="plot_raw" value="AalborgWWTPs-heatmap-group-facet.tsv" ftype="tabular"/>
+        </test>
+        <!-- normalise -->
+        <test expect_num_outputs="1">
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
+            <param name="normalise" value="true"/>
+            <output name="plot" value="AalborgWWTPs-heatmap-normalise.pdf" ftype="pdf"/>
+        </test>
+        <!-- normalise by a specific sample -->
+        <!-- TODO https://github.com/MadsAlbertsen/ampvis2/issues/130 -->
+        <!-- <test expect_num_outputs="1">
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
+            <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 
+            <param name="normalise" value="true"/>
+            <conditional name="normalise_by_cond">
+                <param name="normalise_by_sel" value="sample"/>
+                <param name="normalise_by" value="16SAMP-747"/>
+            </conditional>
+            <output name="plot" value="AalborgWWTPs-heatmap-normalise_by_sample.pdf" ftype="pdf"/>
+        </test> -->
+        <!-- normalise by a metadata variable -->
+        <!-- TODO https://github.com/MadsAlbertsen/ampvis2/issues/130 -->
+        <!-- <test expect_num_outputs="1">
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
+            <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 
+            <param name="group_by" value="Plant"/>
+            <conditional name="normalise_by_cond">
+                <param name="normalise_by_sel" value="variable"/>
+                <param name="normalise_by" value="Plant"/>
+            </conditional>
+            <output name="plot" value="AalborgWWTPs-heatmap-normalise_by_variable.pdf" ftype="pdf"/>
+        </test> -->
+        <!-- tax options -->
+        <test expect_num_outputs="1">
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
+            <param name="tax_aggregate" value="Order"/>
+            <param name="tax_add" value="Class"/>
+            <param name="tax_show" value="5"/>
+            <param name="showRemainingTaxa" value="true"/>
+            <output name="plot" value="AalborgWWTPs-heatmap-tax.pdf" ftype="pdf"/>
+        </test>
+        <!-- sort by a specific sample -->
+        <test expect_num_outputs="1">
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
+            <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 
+            <conditional name="sort_by_cond">
+                <param name="sort_by_sel" value="sample"/>
+                <param name="sort_by" value="16SAMP-747"/>
+            </conditional>
+            <output name="plot" value="AalborgWWTPs-heatmap-sort_by_sample.pdf" ftype="pdf"/>
+        </test>
+        <!-- sort by a group of samples -->
+        <test expect_num_outputs="1">
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
+            <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 
+            <param name="group_by" value="Period"/>
+            <conditional name="sort_by_cond">
+                <param name="sort_by_sel" value="group"/>
+                <param name="sort_by" value="Winter"/>
+            </conditional>
+            <output name="plot" value="AalborgWWTPs-heatmap-sort_by_group.pdf" ftype="pdf"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
+            <param name="tax_aggregate" value="Genus"/>
+            <conditional name="plot_functions_cond">
+                <param name="plot_functions_sel" value="midasfieldguide"/>
+                <param name="functions" value="MiDAS,Filamentous,AOB,NOB,GAO"/>
+            </conditional>
+            <output name="plot" value="AalborgWWTPs-heatmap-plot_foo_midas.pdf" ftype="pdf"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
+            <param name="tax_aggregate" value="Genus"/>
+            <conditional name="plot_functions_cond">
+                <param name="plot_functions_sel" value="file"/>
+                <param name="function_data" value="AalborgWWTPs-functions.tsv" ftype="tsv"/>
+                <param name="functions" value="Foo,Bar"/>
+            </conditional>
+            <output name="plot" value="AalborgWWTPs-heatmap-plot_foo_file.pdf" ftype="pdf"/>
+        </test>
+    
+    </tests>
+    <help><![CDATA[
+What it does
+============
+
+Generates a heatmap of amplicon data by using sample metadata to aggregate
+samples and taxonomy to aggregate OTUs.
+
+The Galaxy tool calls the `amp_heatmap
+<https://madsalbertsen.github.io/ampvis2/reference/amp_heatmap.html>`_ function
+of the ampvis2 package. 
+
+@HELP_RELATIVE_ABUNDANCES@
+
+Input
+=====
+
+@HELP_RDS_INPUT@
+
+@HELP_METADATA_LIST_INPUT@
+
+Funtional data at genus level can be added to the plot. By default the
+information is taken from `midasfieldguide <https://midasfieldguide.org/>`_ but
+it can also be given by a dataset (parameter function_data): 
+
+- The first column must be the Genus names and 
+- any other column(s) can be any property or metabolic function of the individual Genera. 
+
+Output
+======
+
+Heatmap in the chosen output format. 
+If table output is chosen the data presented in the heatmap is written into a tabular dataset.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file