Mercurial > repos > iuc > usher

comparison usher.xml @ 3:746b434c8fbb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 568f7ae147ea
comparison
equal deleted inserted replaced
2:8f6c7638eab2 3:746b434c8fbb
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_TOOL_VERSION@' profile='20.01'>
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='edam_ontology' /> 6 <expand macro="xrefs"/>
7 <expand macro='requirements' /> 7 <expand macro='requirements' />
8 <version_command>usher --version</version_command> 8 <version_command>usher --version</version_command>
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 &&
40 #end if 40 #end if
41 $output_options.write_parsimony_scores_per_node 41 $output_options.write_parsimony_scores_per_node
42 #if $output_options.multiple_placements 42 #if $output_options.multiple_placements
43 -M $output_options.multiple_placements 43 -M $output_options.multiple_placements
44 #end if 44 #end if
45 #if $retain_input_branch_lengths 45 $retain_input_branch_lengths
46 $retain_input_branch_lengths
47 #end if
48 -T \${GALAXY_SLOTS:-1} 46 -T \${GALAXY_SLOTS:-1}
49 -d ./ 47 -d ./
50 #if $output_options.write_subtrees_size 48 #if $output_options.write_subtrees_size
51 && mkdir -p out_subtrees out_subtrees_expanded out_subtrees_mutations 49 && mkdir -p out_subtrees out_subtrees_expanded out_subtrees_mutations
52 && mv subtree*expanded.txt ./out_subtrees_expanded 50 && mv subtree*expanded.txt ./out_subtrees_expanded
297 </output> 295 </output>
298 </test> 296 </test>
299 <test expect_num_outputs="3"> 297 <test expect_num_outputs="3">
300 <param name="vcf" value="new_samples.vcf.gz" ftype="vcf_bgzip"/> 298 <param name="vcf" value="new_samples.vcf.gz" ftype="vcf_bgzip"/>
301 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/> 299 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
302 <param name="retain_input_branch" value="true"/> 300 <param name="retain_input_branch_lengths" value="true"/>
303 <output name="final_tree" file="test_12_final_tree.nh" ftype="newick" lines_diff="2"/> 301 <output name="final_tree" file="test_12_final_tree.nh" ftype="newick" lines_diff="2"/>
304 <output name="mutation_paths" file="test_12_mutation_path.nh" ftype="txt"/> 302 <output name="mutation_paths" file="test_12_mutation_path.nh" ftype="txt"/>
305 <output name="clades" ftype="txt"> 303 <output name="clades" ftype="txt">
306 <assert_contents> 304 <assert_contents>
307 <has_size value="0"/> 305 <has_size value="0"/>