Mercurial > repos > iuc > usher
diff usher.xml @ 4:568f7ae147ea draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd
| author | iuc |
|---|---|
| date | Mon, 02 Feb 2026 14:40:17 +0000 |
| parents | 746b434c8fbb |
| children |
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--- a/usher.xml Sun Mar 17 18:10:07 2024 +0000 +++ b/usher.xml Mon Feb 02 14:40:17 2026 +0000 @@ -1,11 +1,11 @@ -<tool id='usher' name='UShER' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.01'> +<tool id='usher' name='UShER' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' profile='@PROFILE@'> <description>ultrafast sample placement on existing trees</description> <macros> <import>macros.xml</import> </macros> <expand macro="xrefs"/> <expand macro='requirements' /> - <version_command>usher --version</version_command> + <expand macro="version"/> <command detect_errors='exit_code'><![CDATA[ #if $vcf.ext == 'vcf_bgzip': ln -s '$vcf' input.vcf.gz && @@ -47,11 +47,11 @@ -d ./ #if $output_options.write_subtrees_size && mkdir -p out_subtrees out_subtrees_expanded out_subtrees_mutations - && mv subtree*expanded.txt ./out_subtrees_expanded - && mv subtree*mutations.txt ./out_subtrees_mutations + && ( mv subtree*expanded.txt ./out_subtrees_expanded || true ) + && ( mv subtree*mutations.txt ./out_subtrees_mutations || true ) && mv subtree*.nh ./out_subtrees #end if - ]]> </command> +]]> </command> <inputs> <param name="vcf" type="data" format="vcf,vcf_bgzip" label="VCF file" help="Input VCF file."/> <param name="tree" type="data" format="newick" optional="True" label="Tree file" help="Input tree file in Newick format."/> @@ -138,7 +138,7 @@ </section> <output name="annotated_tree" file="test_01_annotated_tree.pb" ftype="protobuf3"> <assert_contents> - <has_size value="26100" delta="100"/> + <has_size value="26800" delta="100"/> </assert_contents> </output> <output name="condensed_tree" file="test_01_condensed_tree.nh" ftype="newick"/> @@ -195,8 +195,8 @@ <output_collection name="subtrees" type="list" count="1"> <element name="subtree-1" file="test_04_subtree_1.nh"/> </output_collection> - <output_collection name="subtrees_expanded" type="list" count="1"> - <element name="subtree-1-expanded" file="test_04_subtree_1_expanded.txt" ftype="txt"/> + <output_collection name="subtrees_expanded" type="list" count="0" > + <!-- <element name="subtree-1-expanded" file="test_04_subtree_1_expanded.txt" ftype="txt"/> --> </output_collection> <output_collection name="subtrees_mutations" type="list" count="1"> <element name="subtree-1-mutations" file="test_04_subtree_1_mutations.txt" ftype="txt"/>