Mercurial > repos > iuc > merge_metaphlan_tables

diff merge_metaphlan_tables.xml @ 12:7f5d7b0e9884 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 70ba929dd55348ee43753e6ae29bd45c5cdf5471
author iuc
date Sat, 10 Feb 2024 23:56:53 +0000
parents e073891b2afc
children
line wrap: on
line diff
--- a/merge_metaphlan_tables.xml	Thu Apr 20 11:26:31 2023 +0000
+++ b/merge_metaphlan_tables.xml	Sat Feb 10 23:56:53 2024 +0000
@@ -7,9 +7,13 @@
     <expand macro="requirements"/>
     <version_command>metaphlan -v</version_command>
     <command detect_errors="aggressive"><![CDATA[
-merge_metaphlan_tables.py
-    #for $element in $inputs
-        '$element'
+    #for $input in $inputs
+        ln -s '$input' '${input.element_identifier}' &&
+    #end for
+
+    merge_metaphlan_tables.py
+    #for $input in $inputs
+        '${input.element_identifier}'
     #end for
     > '$output'
 ]]>
@@ -22,11 +26,12 @@
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="inputs" value="SRS014464-Anterior_nares-abundances.tabular,SRS014464-Anterior_nares-abundances.tabular"/>
+            <param name="inputs" value="SRS014464-Anterior_nares-abundances.tabular,SRS014464-Anterior_nares-abundances-samefiledifferentname.tabular"/>
             <output name="output" ftype="tabular">
                 <assert_contents>
                     <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
-                    <has_text text="dataset_"/>
+                    <has_text text="SRS014464-Anterior_nares-abundances"/>
+                    <has_text text="SRS014464-Anterior_nares-abundances-samefiledifferentname"/>
                     <has_text text="clade_name"/>
                     <has_line_matching expression="#.*"/>
                 </assert_contents>