--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/octave.xml	Fri Aug 16 08:53:46 2024 +0000
@@ -0,0 +1,106 @@
+<tool id="ampvis2_octave" name="ampvis2 octave plot" 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 '$rscript'
+    ]]></command>
+    <configfiles>
+        <configfile name="rscript"><![CDATA[
+            library(ampvis2, quietly = TRUE)
+            d <- readRDS("$data")
+            plot <- amp_octave(
+                d,
+                tax_aggregate = "$tax_aggregate",
+                #if $group_by
+                    group_by = "$group_by",
+                    #if $scales
+                        scales = "$scales",
+                    #end if
+                #end if
+                num_threads = 1
+            )
+            @OUTPUT_TOKEN@
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="rds_metadata_input_macro"/>
+        <expand macro="taxlevel_macro" argument="tax_aggregate" label="Aggregate (sum) OTU's to a taxonomic level initially." help="OTU's that have not been assigned at the chosen level will be removed with a message.">
+            <option value="OTU" selected="true">OTU/ASV</option>
+        </expand>
+        <expand macro="metadata_select" argument="group_by" label="Group the samples based on a metadata variable." help="Variable needs to be categorical/discrete"/>
+        <expand macro="facet_scales_macro" argument="scales" help="Only relevant if for group_by a value is selected"/>
+        <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-octave.pdf" ftype="pdf" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
+            <param name="tax_aggregate" value="Class"/> 
+            <param name="out_format" value="png"/> 
+            <output name="plot" value="AalborgWWTPs-octave.png" ftype="png" 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="Year"/> 
+            <param name="scales" value="free"/> 
+            <param name="out_format" value="svg"/> 
+            <output name="plot" value="AalborgWWTPs-octave.svg" ftype="svg" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+What it does
+============
+
+Generates an octave plot to assess alpha diversity. An octave plot is a
+histogram of the number of taxa observed by bins of read counts, where the bin
+ranges increase exponentially, see details.
+
+The Galaxy tool calls the `amp_octave
+<https://kasperskytte.github.io/ampvis2/reference/amp_octave.html>`_ function
+of the ampvis2 package. 
+
+
+Details
+=======
+
+The n-th bin in the histogram has the range ``r(n)=2n...2n+1-1``. The height of the
+bars then reflect the number of unique taxa with read counts in each bin. By
+judging the distribution one can assess whether the samples have been sequenced
+deeply enough at the chosen taxonomic level. A full symmetrical bell-shaped
+distribution with the left part far from the y-axis is the ideal. A high amount
+of OTU's with a low amount of reads indicates noise, chimeras, and even cross
+talk.
+
+Aggregating OTU's using ``tax_aggregate`` is useful to assess whether the samples
+have been sequenced deep enough to capture the full diversity at the given
+level, but ONLY applies to OTU's that have assigned taxonomy at the given level.
+
+It is recommended to look at samples individually as grouping samples will
+almost always look ideal. It is better to identify "bad" samples individually
+and remove them.
+
+Input
+=====
+
+@HELP_RDS_INPUT@
+
+@HELP_METADATA_LIST_INPUT@
+
+Output
+======
+
+Octave plot in the chosen output format.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file