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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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3:746b434c8fbb 4:568f7ae147ea
1 <tool id='usher' name='UShER' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.01'> 1 <tool id='usher' name='UShER' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' profile='@PROFILE@'>
2 <description>ultrafast sample placement on existing trees</description> 2 <description>ultrafast sample placement on existing trees</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/> 6 <expand macro="xrefs"/>
7 <expand macro='requirements' /> 7 <expand macro='requirements' />
8 <version_command>usher --version</version_command> 8 <expand macro="version"/>
9 <command detect_errors='exit_code'><![CDATA[ 9 <command detect_errors='exit_code'><![CDATA[
10 #if $vcf.ext == 'vcf_bgzip': 10 #if $vcf.ext == 'vcf_bgzip':
11 ln -s '$vcf' input.vcf.gz && 11 ln -s '$vcf' input.vcf.gz &&
12 ln -s '$vcf.metadata.tabix_index' input.vcf.gz.tbi && 12 ln -s '$vcf.metadata.tabix_index' input.vcf.gz.tbi &&
13 #set $input_vcf = 'input.vcf.gz' 13 #set $input_vcf = 'input.vcf.gz'
45 $retain_input_branch_lengths 45 $retain_input_branch_lengths
46 -T \${GALAXY_SLOTS:-1} 46 -T \${GALAXY_SLOTS:-1}
47 -d ./ 47 -d ./
48 #if $output_options.write_subtrees_size 48 #if $output_options.write_subtrees_size
49 && mkdir -p out_subtrees out_subtrees_expanded out_subtrees_mutations 49 && mkdir -p out_subtrees out_subtrees_expanded out_subtrees_mutations
50 && mv subtree*expanded.txt ./out_subtrees_expanded 50 && ( mv subtree*expanded.txt ./out_subtrees_expanded || true )
51 && mv subtree*mutations.txt ./out_subtrees_mutations 51 && ( mv subtree*mutations.txt ./out_subtrees_mutations || true )
52 && mv subtree*.nh ./out_subtrees 52 && mv subtree*.nh ./out_subtrees
53 #end if 53 #end if
54 ]]> </command> 54 ]]> </command>
55 <inputs> 55 <inputs>
56 <param name="vcf" type="data" format="vcf,vcf_bgzip" label="VCF file" help="Input VCF file."/> 56 <param name="vcf" type="data" format="vcf,vcf_bgzip" label="VCF file" help="Input VCF file."/>
57 <param name="tree" type="data" format="newick" optional="True" label="Tree file" help="Input tree file in Newick format."/> 57 <param name="tree" type="data" format="newick" optional="True" label="Tree file" help="Input tree file in Newick format."/>
58 <param argument="--load-mutation-annotated-tree" type="data" format="protobuf3" optional="True" label="Mutation-annotated tree object" help="Load a mutation annotated tree file, in protocol-buffers format (protobuf3)."/> 58 <param argument="--load-mutation-annotated-tree" type="data" format="protobuf3" optional="True" label="Mutation-annotated tree object" help="Load a mutation annotated tree file, in protocol-buffers format (protobuf3)."/>
59 <param name="sort_mode" type="select" label="Mode of sorting new samples"> 59 <param name="sort_mode" type="select" label="Mode of sorting new samples">
136 <section name="output_options"> 136 <section name="output_options">
137 <param name="save_mutation_annotated_tree" value="true" ftype="newick"/> 137 <param name="save_mutation_annotated_tree" value="true" ftype="newick"/>
138 </section> 138 </section>
139 <output name="annotated_tree" file="test_01_annotated_tree.pb" ftype="protobuf3"> 139 <output name="annotated_tree" file="test_01_annotated_tree.pb" ftype="protobuf3">
140 <assert_contents> 140 <assert_contents>
141 <has_size value="26100" delta="100"/> 141 <has_size value="26800" delta="100"/>
142 </assert_contents> 142 </assert_contents>
143 </output> 143 </output>
144 <output name="condensed_tree" file="test_01_condensed_tree.nh" ftype="newick"/> 144 <output name="condensed_tree" file="test_01_condensed_tree.nh" ftype="newick"/>
145 <output name="final_tree" file="test_01_final_tree.nh" ftype="newick"/> 145 <output name="final_tree" file="test_01_final_tree.nh" ftype="newick"/>
146 </test> 146 </test>
193 </assert_contents> 193 </assert_contents>
194 </output> 194 </output>
195 <output_collection name="subtrees" type="list" count="1"> 195 <output_collection name="subtrees" type="list" count="1">
196 <element name="subtree-1" file="test_04_subtree_1.nh"/> 196 <element name="subtree-1" file="test_04_subtree_1.nh"/>
197 </output_collection> 197 </output_collection>
198 <output_collection name="subtrees_expanded" type="list" count="1"> 198 <output_collection name="subtrees_expanded" type="list" count="0" >
199 <element name="subtree-1-expanded" file="test_04_subtree_1_expanded.txt" ftype="txt"/> 199 <!-- <element name="subtree-1-expanded" file="test_04_subtree_1_expanded.txt" ftype="txt"/> -->
200 </output_collection> 200 </output_collection>
201 <output_collection name="subtrees_mutations" type="list" count="1"> 201 <output_collection name="subtrees_mutations" type="list" count="1">
202 <element name="subtree-1-mutations" file="test_04_subtree_1_mutations.txt" ftype="txt"/> 202 <element name="subtree-1-mutations" file="test_04_subtree_1_mutations.txt" ftype="txt"/>
203 </output_collection> 203 </output_collection>
204 </test> 204 </test>