Mercurial > repos > iuc > biom_convert

diff biom_convert.xml @ 12:d4d4e9febf5c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 950bc3657a7bd6975337324bd0f1d0e5c0afc0f4
author iuc
date Fri, 15 Mar 2024 15:26:20 +0000
parents 091bb5922a82
children
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line diff
--- a/biom_convert.xml	Fri Feb 09 21:35:43 2024 +0000
+++ b/biom_convert.xml	Fri Mar 15 15:26:20 2024 +0000
@@ -114,8 +114,8 @@
         <data format="biom1" name="output_fp">
             <change_format>
                 <when input="output.type_selector" value="tsv" format="tabular" />
-                <when input="output.biom_type" value="json" format="biom1" />
-                <when input="output.biom_type" value="hdf5" format="biom2" />
+                <when input="output.biom_type.selector" value="json" format="biom1" />
+                <when input="output.biom_type.selector" value="hdf5" format="biom2" />
             </change_format>
         </data>
     </outputs>
@@ -132,14 +132,31 @@
                 <conditional name="biom_type">
                     <param name="selector" value="json"/>
                 </conditional>
-                <param name="sample_metadata_fp"/>
-                <param name="observation_metadata_fp"/>
             </conditional>
             <output name="output_fp" file="output_taxonomy_1.biom1.re" ftype="biom1" compare="re_match"/>
         </test>
         <test>
             <conditional name="input">
                 <param name="type_selector" value="tsv"/>
+                <param name="input_fp" value="input_abundance_taxonomy_1.tabular" ftype="tabular"/>
+                <param name="process_obs_metadata" value="taxonomy"/>
+            </conditional>
+            <conditional name="output">
+                <param name="type_selector" value="biom"/>
+                <param name="table_type" value="OTU table"/>
+                <conditional name="biom_type">
+                    <param name="selector" value="hdf5"/>
+                </conditional>
+            </conditional>
+            <output name="output_fp" ftype="biom2">
+                <assert_contents>
+                    <has_size value="37k" delta="10k"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <conditional name="input">
+                <param name="type_selector" value="tsv"/>
                 <param name="input_fp" value="input_abundance_1.tabular" ftype="tabular"/>
                 <param name="process_obs_metadata" value=""/>
             </conditional>