diff tree_macros.xml @ 0:cd7675c5b15a draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tree_macros.xml	Wed Feb 04 13:15:55 2026 +0000
@@ -0,0 +1,37 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TREE_CMD_LINE@">
+        tree.py
+            --input-fasta '$input_fasta'
+            --input-biom '$input_biom'
+            @CPUS@
+            --output-tree '$output_tree'
+            --html '$html'
+    </token>
+
+    <xml name="tree_inputs">
+        <!-- Files -->
+        <param argument="--input-fasta" type="data" format="fasta" label="Sequence file (.fasta)" help="FASTA file containing the representative sequences to be used for phylogenetic tree construction." />
+        <param argument="--input-biom" type="data" format="biom1" label="Abundance file (.biom)" help="BIOM file containing the abundance table associated with the input sequences." />
+    </xml>
+
+    <!-- Test -->
+    <xml name="tree_test_input">
+        <param name="input_fasta" value="references/04-filters.fasta" />
+        <param name="input_biom" value="references/06-affiliation.biom" />
+    </xml>
+
+    <xml name="tree_test_output">
+        <output name="output_tree" file="references/15-tree-mafft.nwk" compare="sim_size" delta="30"/>
+        <output name="html" file="references/15-tree-mafft.html" compare="diff" lines_diff="2" />
+        <output name="html">
+            <assert_contents>
+                <has_text_matching expression="FROGS\sTree" />
+                <has_text_matching expression="abundance_removed.*:\s0" />
+                <has_text_matching expression="abundance_kept.*:\s73531" />
+                <has_text_matching expression="asv_removed.*:\s0" />
+                <has_text_matching expression="asv_kept.*:\s54" />
+            </assert_contents>
+        </output>
+    </xml>
+</macros>