diff phyloseq_structure_macros.xml @ 0:6507a8d42a4f draft default tip

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 78ca62b54aee22893d278d9c3d495527be405f8a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_structure_macros.xml	Wed Feb 04 13:16:44 2026 +0000
@@ -0,0 +1,49 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@PHYLOSEQ_STRUCTURE_CMD_LINE@">
+    phyloseq_structure.py
+        --phyloseq-rdata '$phyloseq_rdata'
+        --beta-distance-matrix '$beta_distance_matrix'
+        --var-exp '$var_exp'
+        --ordination-method '$ordination_method'
+        --html '$html'
+    </token>
+
+    <xml name="phyloseq_structure_inputs">
+        <!-- Files -->
+        <param argument="--phyloseq-rdata" type="data" format="rdata" label="Phyloseq object (.Rdata)" help="RData file generated by the FROGS Stat 'Phyloseq Import data' tool."/>
+        <param argument="--beta-distance-matrix" type="data" format="tsv" label="Beta diversity distance matrix file" help="TSV file generated by the FROGS Stat 'Phyloseq Beta Diversity' tool."/>
+		<!-- Parameters -->
+		<param argument="--var-exp" type="text" label="Grouping variable" help="Experimental variable used to group samples in the ordination plots (e.g., Treatment, Site, Host type, etc.)." optional="false" value="" >
+            <expand macro="restricted_sanitizer_validator"/>
+        </param>
+		<param argument="--ordination-method" type="select" label="Ordination method" help="Ordination method used to visualize sample relationships based on beta diversity distances (e.g., PCoA, NMDS, DPCoA).">
+			<option value="MDS" >MDS/PCoA</option>
+			<option value="NMDS" >NMDS</option>
+            <option value="DPCoA" >DPCoA</option>
+        </param>
+    </xml>
+
+    <!-- Test -->
+    <xml name="phyloseq_structure_test_input">
+        <param name="phyloseq_rdata" value="references/16-phylo_import.Rdata" />
+        <param name="var_exp" value="EnvType" />
+		<param name="beta_distance_matrix" value="references/unifrac.tsv"/>
+        <param name="ordination_method" value="MDS" />
+    </xml>
+
+    <xml name="phyloseq_structure_test_output">
+        <output name="html" count="1">
+            <assert_contents>
+                <!-- HTML size or line diff can't be used as many information about path, os, date are present. -->
+                <!-- Here we test only title, intermediate results and output of last R command -->
+                <has_text text='Stat: Structure Visualisation' />
+                <has_text text='(phyloseq_structure.py' />
+				<has_text text='v5.1.0)' />
+                <has_text text='"title":{"text":"Axis.1   [22.1%]' />
+                <has_text text='"title":{"text":"Axis.2   [12.8%]' />
+                <has_text text='─ Session info ───────────────────────────────────────────────────────────────' />
+            </assert_contents>
+        </output>
+    </xml>
+</macros>