diff core.xml @ 0:48e343a308b0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/core.xml	Mon Apr 04 10:28:11 2022 +0000
@@ -0,0 +1,95 @@
+<tool id="ampvis2_core" name="ampvis2 core community analysis" 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 '$rscript'
+    ]]></command>
+    <configfiles>
+        <configfile name="rscript"><![CDATA[
+            library(ampvis2, quietly = TRUE)
+            data <- readRDS("$data")
+            #set group_by_list='c("' + '", "'.join(str($group_by).split(",")) + '")'
+            plot <- amp_core(
+                data,
+                group_by = $group_by_list,
+                core_pct = $core_pct,
+                margin_plots = "$margin_plots",
+                margin_plot_values_size = $margin_plot_values_size,
+                widths = c($widths, 1),
+                heights = c(1, $heights)
+            )
+            @OUTPUT_TOKEN@
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="rds_metadata_input_macro"/>
+        <expand macro="metadata_select_discrete" argument="group_by" optional="false" multiple="true" label="Variable(s) which contain the desired grouping of samples" help="Can also be done by sample, just provide the name of the variable containing unique sample ID's"/>
+        <param argument="core_pct" type="float" value="80" min="0" max="100" label="Threshold in percent" help="Threshold for defining abundant (a.k.a. core) OTU's for each group"/>
+        <param argument="margin_plots" type="select" label="Margin plots to show" help="Margin plots display the cumulative read abundances of all OTU's per group sharing either x or y axis with the main plot">
+            <option value="x">Only show x-axis margin plot</option>
+            <option value="y">Only show y-axis margin plot</option>
+            <option value="xy" selected="true">Show both x and y-axis margin plots</option>
+            <option value="">Don't show any margin plots</option>
+        </param>
+        <param argument="margin_plot_values_size" type="integer" value="3" min="0" label="The size of the values" help="As indicated in the margin plots on top of the bars. Set to 0 to disable."/>
+        <param argument="widths" type="integer" value="5" min="1" label="Relative width of the main and y margin plots"/>
+        <param argument="heights" type="integer" value="5" min="1" label="Relative widths of the main and x margin plots"/>
+        <expand macro="out_format_macro"/>
+    </inputs>
+    <outputs>
+        <expand macro="out_macro"/>
+    </outputs>
+    <tests>
+        <!-- defaults -->
+        <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"/> 
+            <output name="plot" value="AalborgWWTPs-core.pdf" ftype="pdf"/>
+        </test>
+        <!--multiple groups + non-default widths / heights-->
+        <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,Period"/> 
+            <param name="core_pct" value="90"/>
+            <param name="widths" value="4"/>
+            <param name="heights" value="4"/>
+            <output name="plot" value="AalborgWWTPs-core-multiple.pdf" ftype="pdf"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+What it does
+============
+
+Core community plot to investigate how many of the most abundant OTU's comprise
+the "core" of groups of samples, their abundances etc.
+
+The Galaxy tool calls the `amp_core
+<https://madsalbertsen.github.io/ampvis2/reference/amp_core.html>`_ function
+of the ampvis2 package.
+
+This analysis only makes sense without aggregating OTU's to any taxonomic level,
+or else it will be biased by taxonomy and only be done on OTU's that have been
+classified, which is rarely all.
+
+
+@HELP_RELATIVE_ABUNDANCES@
+
+Input
+=====
+
+@HELP_RDS_INPUT@
+
+@HELP_METADATA_LIST_INPUT@
+
+Output
+======
+
+A core community plot in the chosen output format.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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