# HG changeset patch
# User bgruening
# Date 1699124401 0
# Node ID 2c87f56bd53a5419d87747705c6e2d993d788d75
# Parent  370b56f8a02d71372fede1e7fa2365ebea52bd0a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5

diff -r 370b56f8a02d -r 2c87f56bd53a format_metaphlan2_output.xml
--- a/format_metaphlan2_output.xml	Wed Oct 19 14:39:16 2022 +0000
+++ b/format_metaphlan2_output.xml	Sat Nov 04 19:00:01 2023 +0000
@@ -1,8 +1,10 @@
 <tool id="format_metaphlan2_output" name="Format MetaPhlAn2" version="0.2.0">
     <description>output to extract abundance at different taxonomic levels</description>
-
     <requirements>
     </requirements>
+    <xrefs>
+        <xref type="bio.tools">format_metaphlan2_output</xref>
+    </xrefs>
 
     <stdio>
     </stdio>
@@ -10,23 +12,21 @@
     <version_command></version_command>
 
     <command><![CDATA[
-        python $__tool_directory__/format_metaphlan2_output.py
-            --metaphlan2_output $input_file
-            --all_taxo_level_abundance_file $all_taxo_level_abundance_file
-            --kingdom_abundance_file $kingdom_abundance_file
-            --phylum_abundance_file $phylum_abundance_file
-            --class_abundance_file $class_abundance_file
-            --order_abundance_file $order_abundance_file
-            --family_abundance_file $family_abundance_file
-            --genus_abundance_file $genus_abundance_file
-            --species_abundance_file $species_abundance_file
-            --strains_abundance_file $strains_abundance_file
+        python '$__tool_directory__/format_metaphlan2_output.py'
+            --metaphlan2_output '$input_file'
+            --all_taxo_level_abundance_file '$all_taxo_level_abundance_file'
+            --kingdom_abundance_file '$kingdom_abundance_file'
+            --phylum_abundance_file '$phylum_abundance_file'
+            --class_abundance_file '$class_abundance_file'
+            --order_abundance_file '$order_abundance_file'
+            --family_abundance_file '$family_abundance_file'
+            --genus_abundance_file '$genus_abundance_file'
+            --species_abundance_file '$species_abundance_file'
+            --strains_abundance_file '$strains_abundance_file'
     ]]></command>
-
     <inputs>
         <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="Output file of MetaPhlAN with all taxonomic levels (from kingdom to strains, --metaphlan2_output)"/>
     </inputs>
-
     <outputs>
         <data name="all_taxo_level_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Abundances for all taxonomic levels" />
         <data name="kingdom_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Kingdom abundances" />
@@ -64,4 +64,4 @@
 
     <citations>
     </citations>
-</tool>
\ No newline at end of file
+</tool>