# HG changeset patch
# User iuc
# Date 1639929165 0
# Node ID 52fd1d49141764948fe67b10fb0a3a8ff065f166
# Parent  79e2ee4e6ebb274e17e0d865b2bc034f4aec0ddd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79"

diff -r 79e2ee4e6ebb -r 52fd1d491417 matutils.xml
--- a/matutils.xml	Tue May 11 17:54:51 2021 +0000
+++ b/matutils.xml	Sun Dec 19 15:52:45 2021 +0000
@@ -296,7 +296,7 @@
     </outputs>
     <tests>
         <test expect_num_outputs="3">
-            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
+            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
             <conditional name="matutils_mode">
                 <param name="options_mode" value="extract"/>
                 <param name="resolve_polytomies" value="true"/>
@@ -312,7 +312,7 @@
             <output name="path_clades" file="test_13_path_clades.tabular" ftype="tabular"/>
         </test>
         <test expect_num_outputs="5">
-            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
+            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
             <conditional name="matutils_mode">
                 <param name="options_mode" value="extract"/>
                 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/>
@@ -332,7 +332,7 @@
             </output>
         </test>
         <test expect_num_outputs="4">
-            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
+            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
             <conditional name="matutils_mode">
                 <param name="options_mode" value="extract"/>
                 <param name="outputs_extract" value="write-vcf-no-genotypes,write-mat,write-json,write-tree"/>
@@ -347,7 +347,7 @@
             <output name="tree_newick" file="test_15_tree.nh" ftype="newick"/>
         </test>
         <test expect_num_outputs="3">
-            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
+            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
             <conditional name="matutils_mode">
                 <param name="options_mode" value="extract"/>
                 <param name="outputs_extract" value="used-samples,sample-paths,write-vcf"/>
@@ -365,7 +365,7 @@
             </output>
         </test>
         <test expect_num_outputs="5">
-            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
+            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
             <conditional name="matutils_mode">
                 <param name="options_mode" value="extract"/>
                 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/>
@@ -385,7 +385,7 @@
             </output>
         </test>
         <test expect_num_outputs="5">
-            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
+            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
             <conditional name="matutils_mode">
                 <param name="options_mode" value="extract"/>
                 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/>
@@ -405,7 +405,7 @@
             </output>
         </test>
         <test expect_num_outputs="3">
-            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
+            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
             <conditional name="matutils_mode">
                 <param name="options_mode" value="extract"/>
                 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths"/>
@@ -419,7 +419,7 @@
             <output name="path_clades" file="test_19_path_clades.tabular" ftype="tabular"/>
         </test>
         <test expect_num_outputs="1">
-            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
+            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
             <conditional name="matutils_mode">
                 <param name="options_mode" value="summary"/>
                 <param name="summary_options" value="general"/>
@@ -427,7 +427,7 @@
             <output name="general_stats" file="test_20_general_stats.txt" ftype="txt"/>
         </test>
         <test expect_num_outputs="4">
-            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
+            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
             <conditional name="matutils_mode">
                 <param name="options_mode" value="summary"/>
                 <param name="summary_options" value="samples,clades,mutations,aberrant"/>
@@ -438,7 +438,7 @@
             <output name="aberrant_stats" file="test_21_aberrant_stats.tabular" ftype="tabular"/>       
         </test>
         <test expect_num_outputs="1">
-            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
+            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
             <conditional name="matutils_mode">
                 <param name="options_mode" value="uncertainty"/>
                 <param name="samples" value="sample_names.txt"/>
@@ -447,7 +447,7 @@
             <output name="total_parsimony_tree" file="test_22_total_parsimony_tree.txt" ftype="txt"/>
         </test>
         <test expect_num_outputs="2">
-            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
+            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
             <conditional name="matutils_mode">
                 <param name="options_mode" value="uncertainty"/>
                 <param name="samples" value="sample_names.txt"/>
@@ -457,7 +457,7 @@
             <output name="neighbourhood" file="test_23_neighbourhood.tabular" ftype="tabular"/>
         </test>
         <test expect_num_outputs="1">
-            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
+            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
             <conditional name="matutils_mode">
                 <param name="options_mode" value="mask"/>
                 <param name="restricted_samples" value="sample_names.txt"/>
@@ -466,7 +466,7 @@
             <output name="output_mat" file="test_24_restricted.pb" ftype="protobuf3"/>
         </test>
         <test expect_num_outputs="1">
-            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
+            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
             <conditional name="matutils_mode">
                 <param name="options_mode" value="mask"/>
                 <param name="rename_samples" value="rename_samples.tabular"/>
diff -r 79e2ee4e6ebb -r 52fd1d491417 test-data/rename_samples.tabular
--- a/test-data/rename_samples.tabular	Tue May 11 17:54:51 2021 +0000
+++ b/test-data/rename_samples.tabular	Sun Dec 19 15:52:45 2021 +0000
@@ -1,4 +1,4 @@
-England/BRIS-1853249/2020|20-04-02  Spain/BRIS-1853249/2020|20-04-02
-Wales/PHWC-25B04/2020|20-03-24  Spain/BRIS-1853249/2020|20-04-02
-NPL/61-TW/2020|MT072688.1|20-01-13  Spain/BRIS-1853249/2020|20-04-02
-Wales/LIVE-A6831/2020|20-03-16  Spain/BRIS-1853249/2020|20-04-02
\ No newline at end of file
+England/BRIS-1853249/2020|20-04-02	Spain/BRIS-1853249/2020|20-04-02
+Wales/PHWC-25B04/2020|20-03-24	Spain/BRIS-1853249/2020|20-04-02
+NPL/61-TW/2020|MT072688.1|20-01-13	Spain/BRIS-1853249/2020|20-04-02
+Wales/LIVE-A6831/2020|20-03-16	Spain/BRIS-1853249/2020|20-04-02