diff fastreer_vcf2tree.xml @ 0:5ea9b32aaef6 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastreer commit 6e38d3e17b87a9e9804bd90fa2dba708c2361a0b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastreer_vcf2tree.xml	Mon Nov 03 09:28:03 2025 +0000
@@ -0,0 +1,37 @@
+<tool id="fastreer_vcf2tree" name="VCF2TREE" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Newick tree from VCF files</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+        fastreeR VCF2TREE 
+        #for $f in $input_vcfs:
+            -i '$f'
+        #end for
+        -o '$output'
+        -b $bootstraps
+        --threads \${GALAXY_SLOTS:-1}
+        --verbose
+    ]]></command>
+    <inputs>
+        <param name="input_vcfs" type="data" format="vcf,vcf_bgzip" multiple="true" label="VCF input files" help="VCF input files"/>
+        <param name="bootstraps" type="integer" min="0" value="0" label="Number of bootstrap replicates" help="Number of bootstrap replicates"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="newick" label="Output Tree"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_vcfs" value="test.vcf"/>
+            <param name="bootstraps" value="0"/>
+            <output name="output" file="expected.vcf.nwk"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Computes a phylogenetic tree from one or more VCF files using neighbor-joining.
+        Optional parameter for bootsrapping support calculation.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>