Mercurial > repos > iuc > usher
changeset 3:746b434c8fbb draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 5de7b91f2bda9c351f9512601f899248b7278924
| author | iuc |
|---|---|
| date | Sun, 17 Mar 2024 18:10:07 +0000 |
| parents | 8f6c7638eab2 |
| children | |
| files | macros.xml usher.xml |
| diffstat | 2 files changed, 7 insertions(+), 12 deletions(-) [+] |
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--- a/macros.xml Sun Dec 19 15:53:23 2021 +0000 +++ b/macros.xml Sun Mar 17 18:10:07 2024 +0000 @@ -1,13 +1,10 @@ <macros> <token name="@TOOL_VERSION@">0.2.1</token> <token name="@GALAXY_TOOL_VERSION@">galaxy0</token> - <xml name="edam_ontology"> - <edam_topics> - <edam_topic>topic_0194</edam_topic> - </edam_topics> - <edam_operations> - <edam_operation>operation_0540</edam_operation> - </edam_operations> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">usher</xref> + </xrefs> </xml> <xml name="requirements"> <requirements>
--- a/usher.xml Sun Dec 19 15:53:23 2021 +0000 +++ b/usher.xml Sun Mar 17 18:10:07 2024 +0000 @@ -3,7 +3,7 @@ <macros> <import>macros.xml</import> </macros> - <expand macro='edam_ontology' /> + <expand macro="xrefs"/> <expand macro='requirements' /> <version_command>usher --version</version_command> <command detect_errors='exit_code'><![CDATA[ @@ -42,9 +42,7 @@ #if $output_options.multiple_placements -M $output_options.multiple_placements #end if - #if $retain_input_branch_lengths - $retain_input_branch_lengths - #end if + $retain_input_branch_lengths -T \${GALAXY_SLOTS:-1} -d ./ #if $output_options.write_subtrees_size @@ -299,7 +297,7 @@ <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" ftype="protobuf3"/> - <param name="retain_input_branch" value="true"/> + <param name="retain_input_branch_lengths" 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"/> <output name="clades" ftype="txt">