diff venn.xml @ 0:36d4584a5ceb 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/venn.xml	Mon Apr 04 10:17:34 2022 +0000
@@ -0,0 +1,84 @@
+<tool id="ampvis2_venn" name="ampvis2 venn diagram" 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")
+            plot <- amp_venn(
+                data,
+                #if $group_by
+                    group_by = "$group_by",
+                #end if
+                cut_a = $cut_a,
+                cut_f = $cut_f,
+                text_size = $text_size,
+                normalise = $normalise,
+                ## detailed_output = TRUE seems not supported yet https://github.com/MadsAlbertsen/ampvis2/issues/132
+                )
+            ## names(plot)
+            @OUTPUT_TOKEN@
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="rds_metadata_input_macro"/>
+        <expand macro="metadata_select_discrete" argument="group_by" label="Group the data by" halp="Currently only supports a maximum of 3 different groups.">
+            <validator type="expression" message="A maximum of 3 different groups is supported"><![CDATA[len(str(value).split(",")) < 4]]></validator>
+        </expand>
+        <param argument="cut_a" type="float" value="0.1" min="0" max="100" label="Abundance cutoff (percent)" help="OTU's below this abundance are excluded from the analysis"/>
+        <param argument="cut_f" type="float" value="80" min="0" max="100" label="Frequency cutoff (percent)" help="OTU's within the top cut_f of the reads are considered a core OTU"/>
+        <param argument="text_size" type="integer" value="5" min="1" label="Size of the plotted text."/>
+        <expand macro="normalise_macro"/>
+        <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"/> 
+            <output name="plot" value="AalborgWWTPs-venn.pdf" ftype="pdf"/>
+        </test>
+        <!-- defaults + group_by -->
+        <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"/>
+            <output name="plot" value="AalborgWWTPs-venn-group.pdf" ftype="pdf"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+What it does
+============
+
+Calculates the number of "core" OTUs shared by groups given thresholds for how
+frequent the OTUs should be above a certain abundance. Also returns the average
+abundance of the OTUs in a particular group.
+
+The Galaxy tool calls the `amp_venn
+<https://madsalbertsen.github.io/ampvis2/reference/amp_venn.html>`_ function
+of the ampvis2 package.
+
+@HELP_RELATIVE_ABUNDANCES@
+
+Input
+=====
+
+@HELP_RDS_INPUT@
+
+@HELP_METADATA_LIST_INPUT@
+
+Output
+======
+
+A venn diagram in the chosen output format.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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