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Changeset 2:8f6c7638eab2 (2021-12-19)

Previous changeset 1:335665e15630 (2021-09-22) Next changeset 3:746b434c8fbb (2024-03-17)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79"

modified:
test-data/rename_samples.tabular
usher.xml

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

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

[

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