# HG changeset patch
# User iuc
# Date 1639929203 0
# Node ID 8f6c7638eab2ad956997a30ceb4308415f64e979
# Parent  335665e15630c1006883f54799da5fad11391963
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79"

diff -r 335665e15630 -r 8f6c7638eab2 test-data/rename_samples.tabular
--- a/test-data/rename_samples.tabular	Wed Sep 22 21:01:36 2021 +0000
+++ b/test-data/rename_samples.tabular	Sun Dec 19 15:53:23 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
diff -r 335665e15630 -r 8f6c7638eab2 usher.xml
--- a/usher.xml	Wed Sep 22 21:01:36 2021 +0000
+++ b/usher.xml	Sun Dec 19 15:53:23 2021 +0000
@@ -101,15 +101,15 @@
             <filter>output_options['save_mutation_annotated_tree'] is False and output_options['write_parsimony_scores_per_node'] is False</filter>        
         </data>
         <collection name='subtrees' type='list' label='${tool.name} on ${on_string}: subtrees'>
-            <discover_datasets pattern='__designation_and_ext__' format="newick" directory='out_subtrees'/>
+            <discover_datasets pattern='(?P&lt;designation&gt;.*)\.nh' format="newick" directory='out_subtrees'/>
             <filter>output_options['write_subtrees_size']</filter> 
         </collection>
         <collection name='subtrees_expanded' type='list' label='${tool.name} on ${on_string}: subtrees expanded'>
-            <discover_datasets pattern='__designation_and_ext__' format='txt' directory='out_subtrees_expanded'/>
+            <discover_datasets pattern='(?P&lt;designation&gt;.*)\.txt' format='txt' directory='out_subtrees_expanded'/>
             <filter>output_options['write_subtrees_size']</filter> 
         </collection>  
         <collection name='subtrees_mutations' type='list' label='${tool.name} on ${on_string}: subtrees mutations'>
-            <discover_datasets pattern='__designation_and_ext__' format='txt' directory='out_subtrees_mutations'/>
+            <discover_datasets pattern='(?P&lt;designation&gt;.*)\.txt' format='txt' directory='out_subtrees_mutations'/>
             <filter>output_options['write_subtrees_size']</filter> 
         </collection>
         <data name="current_tree" format="newick" from_work_dir="current-tree.nh" label="${tool.name} on ${on_string}: current tree">
@@ -131,12 +131,12 @@
     <tests>
         <test expect_num_outputs="3">
             <param name="vcf" value="global_samples.vcf.gz" ftype="vcf_bgzip" />
-            <param name="tree" value="global_phylo.nh"/>
+            <param name="tree" value="global_phylo.nh" ftype="newick"/>
             <section name="collapse_options">
                 <param name="collapse_tree" value="true"/>
             </section>
             <section name="output_options">
-                <param name="save_mutation_annotated_tree" value="true"/>
+                <param name="save_mutation_annotated_tree" value="true" ftype="newick"/>
             </section>
             <output name="annotated_tree" file="test_01_annotated_tree.pb" ftype="protobuf3">
                 <assert_contents>
@@ -148,7 +148,7 @@
         </test>
         <test expect_num_outputs="3">
             <param name="vcf" value="new_samples.vcf.gz"/>
-            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>
+            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
             <section name="output_options">
                 <param name="write_uncondensed_final_tree" value="true"/>
             </section>
@@ -162,7 +162,7 @@
         </test>
         <test expect_num_outputs="4">
             <param name="vcf" value="global_samples.vcf.gz" ftype="vcf_bgzip" />
-            <param name="tree" value="global_phylo.nh"/>
+            <param name="tree" value="global_phylo.nh" ftype="newick"/>
             <param name="sort_mode" value="--sort-before-placement-1"/>
             <section name="collapse_options">
                 <param name="collapse_tree" value="true"/>
@@ -182,7 +182,7 @@
         </test>
         <test expect_num_outputs="6">
             <param name="vcf" value="new_samples.vcf.gz"/>
-            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>
+            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
             <section name="output_options">
                 <param name="write_uncondensed_final_tree" value="true"/>
                 <param name="write_subtrees_size" value="20"/>
@@ -206,7 +206,7 @@
         </test>
         <test expect_num_outputs="2">
             <param name="vcf" value="new_samples.vcf.gz"/>
-            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>
+            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
             <section name="output_options">
                 <param name="write_parsimony_scores_per_node" value="true"/>
             </section>
@@ -215,7 +215,7 @@
         </test>
         <test expect_num_outputs="3">
             <param name="vcf" value="new_samples.vcf.gz"/>
-            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>  
+            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>  
             <section name="output_options">
                 <param name="multiple_placements" value="2"/>
             </section>
@@ -229,7 +229,7 @@
         </test>
         <test expect_num_outputs="6">
             <param name="vcf" value="new_samples.vcf.gz"/>
-            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>  
+            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>  
             <section name="output_options">
                 <param name="write_single_subtree" value="2"/>
             </section>
@@ -250,7 +250,7 @@
         </test>
         <test expect_num_outputs="3">
             <param name="vcf" value="new_samples.vcf.gz"/>
-            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>
+            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
             <param name="sort_mode" value="--sort-before-placement-2"/>
             <output name="final_tree" file="test_08_final_tree.nh" ftype="newick"/>
             <output name="mutation_paths" file="test_08_mutation_path.nh" ftype="txt"/>
@@ -262,7 +262,7 @@
         </test>
         <test expect_num_outputs="3">
             <param name="vcf" value="new_samples.vcf.gz"/>
-            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>
+            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
             <param name="sort_mode" value="--sort-before-placement-3"/>
             <output name="final_tree" file="test_09_final_tree.nh" ftype="newick"/>
             <output name="mutation_paths" file="test_09_mutation_path.nh" ftype="txt"/>
@@ -274,7 +274,7 @@
         </test>
         <test expect_num_outputs="3">
             <param name="vcf" value="new_samples.vcf.gz"/>
-            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>
+            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
             <param name="sort_mode" value="--sort-before-placement-1 --reverse-sort"/>
             <output name="final_tree" file="test_10_final_tree.nh" ftype="newick"/>
             <output name="mutation_paths" file="test_10_mutation_path.nh" ftype="txt"/>
@@ -286,7 +286,7 @@
         </test>
         <test expect_num_outputs="3">
             <param name="vcf" value="new_samples.vcf.gz"/>
-            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>
+            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
             <param name="sort_mode" value="--sort-before-placement-2 --reverse-sort"/>
             <output name="final_tree" file="test_11_final_tree.nh" ftype="newick"/>
             <output name="mutation_paths" file="test_11_mutation_path.nh" ftype="txt"/>
@@ -298,7 +298,7 @@
         </test>
         <test expect_num_outputs="3">
             <param name="vcf" value="new_samples.vcf.gz" ftype="vcf_bgzip"/>
-            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>
+            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
             <param name="retain_input_branch" value="true"/>
             <output name="final_tree" file="test_12_final_tree.nh" ftype="newick" lines_diff="2"/>
             <output name="mutation_paths" file="test_12_mutation_path.nh" ftype="txt"/>