diff rankabundance.xml @ 0:132d2a794152 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/rankabundance.xml	Mon Apr 04 10:20:48 2022 +0000
@@ -0,0 +1,77 @@
+<tool id="ampvis2_rankabundance" name="ampvis2 rank abundance 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 '$rscript'
+    ]]></command>
+    <configfiles>
+        <configfile name="rscript"><![CDATA[
+            library(ampvis2, quietly = TRUE)
+            data <- readRDS("$data")
+            plot <- amp_rankabundance(
+                data,
+                group_by = "$group_by",
+                showSD = $showSD,
+                log10_x = $log10_x
+            )
+            @OUTPUT_TOKEN@
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="rds_metadata_input_macro"/>
+        <expand macro="metadata_select_discrete" argument="group_by" optional="false" label="Group the samples by"/>
+        <param argument="showSD" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Show standard deviation"/>
+        <param argument="log10_x" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Log10-transform the x-axis" help="Often most variation is observed among the most abundant OTU's, log10-transforming the x-axis will highlight this better."/>
+        <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="Plant"/>
+            <output name="plot" value="AalborgWWTPs-rankabundance.pdf" ftype="pdf"/>
+        </test>
+        <!-- non-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="Plant"/>
+            <param name="showSD" value="false"/>
+            <param name="log10_x" value="false"/>
+            <output name="plot" value="AalborgWWTPs-rankabundance-nondefault.pdf" ftype="pdf"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+What it does
+============
+
+Generates a rank abundance curve (rank abundance vs cumulative read abundance),
+optionally with standard deviation from mean intervals.
+
+The Galaxy tool calls the `amp_rankabundance
+<https://madsalbertsen.github.io/ampvis2/reference/amp_rankabundance.html>`_ function
+of the ampvis2 package.
+
+Currently only OTU level is supported.
+
+Input
+=====
+
+@HELP_RDS_INPUT@
+
+@HELP_METADATA_LIST_INPUT@
+
+Output
+======
+
+An rank abundance plot in the chosen output format.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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