usher_matutils: matutils.xml annotate

annotate matutils.xml @ 2:daa704d3ac8f 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 14:37:36 +0000
parents	75e51e947a98
children

rev	line source
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	1 <tool id='usher_matutils' name='UShER matUtils' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' profile='@PROFILE@'>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	2 <description>analyze, edit, and manipulate mutation annotated tree files</description>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	3 <macros>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	4 <import>macros.xml</import>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	5 </macros>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	6 <expand macro="xrefs"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	7 <expand macro='requirements' />
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	8 <expand macro="version"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	9 <command detect_errors='exit_code'><![CDATA[
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	10 ## get correct extension filenames
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	11 ln -sf '$mutation_annotation_file' '$mutation_annotation_file.element_identifier' &&
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	12
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	13 matUtils
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	14 $matutils_mode.options_mode
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	15 --input-mat '$mutation_annotation_file.element_identifier'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	16
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	17 #if $matutils_mode.options_mode == 'extract'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	18 #if $matutils_mode.operation_mode.operation == 'samples'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	19 #if $matutils_mode.operation_mode.samples
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	20 --samples '${matutils_mode.operation_mode.samples}'
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	21 #end if
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	22 $matutils_mode.operation_mode.prune
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	23 #elif $matutils_mode.operation_mode.operation == 'clade'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	24 --clade '${matutils_mode.operation_mode.clade}'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	25 $matutils_mode.operation_mode.prune
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	26 #elif $matutils_mode.operation_mode.operation == 'mutation'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	27 --mutation '${matutils_mode.operation_mode.mutation}'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	28 $matutils_mode.operation_mode.prune
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	29 #elif $matutils_mode.operation_mode.operation == 'max-epps'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	30 --max-epps $matutils_mode.operation_mode.max_epps
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	31 $matutils_mode.operation_mode.prune
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	32 #elif $matutils_mode.operation_mode.operation == 'max-parsimony'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	33 --max-parsimony $matutils_mode.operation_mode.max_parsimony
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	34 $matutils_mode.operation_mode.prune
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	35 #elif $matutils_mode.operation_mode.operation == 'nearest-k'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	36 --nearest-k '${matutils_mode.operation_mode.nearest_k}'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	37 $matutils_mode.operation_mode.prune
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	38 #elif $matutils_mode.operation_mode.operation == 'max-branch-length'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	39 --max-branch-length $matutils_mode.operation_mode.max_branch_length
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	40 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	41 $matutils_mode.get_representative
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	42 $matutils_mode.resolve_polytomies
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	43 #if 'used-samples' in $matutils_mode.outputs_extract
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	44 --used-samples selected_samples.txt ##$selected_samples
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	45 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	46 #if 'sample-paths' in $matutils_mode.outputs_extract
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	47 --sample-paths path_mutations.tabular ##$path_mutations
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	48 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	49 #if 'clade-paths' in $matutils_mode.outputs_extract
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	50 --clade-paths path_clades.tabular ##$path_clades
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	51 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	52 #if 'all-paths' in $matutils_mode.outputs_extract
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	53 --all-paths all_paths.txt ##$all_paths
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	54 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	55 #if 'write-vcf' in $matutils_mode.outputs_extract
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	56 --write-vcf subtree_vcf.vcf ##$subtree_vcf
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	57 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	58 #if 'write-vcf-no-genotypes' in $matutils_mode.outputs_extract and 'write-vcf' not in $matutils_mode.outputs_extract
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	59 --write-vcf subtree_vcf_no_genotypes.vcf --no-genotypes
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	60 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	61 #if 'write-mat' in $matutils_mode.outputs_extract
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	62 --write-mat mutation_annotated.pb ##$mutation_annotated
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	63 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	64 #if 'write-mat-collapsed' in $matutils_mode.outputs_extract and 'write-mat' not in $matutils_mode.outputs_extract
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	65 --write-mat mutation_annotated_collapsed.pb --collapsed-tree
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	66 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	67 #if 'write-json' in $matutils_mode.outputs_extract
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	68 --write-json subtree_json.json ##$subtree_json
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	69 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	70 #if 'write-tree' in $matutils_mode.outputs_extract
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	71 --write-tree tree_newick.nh ##$tree_newick
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	72 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	73 #if 'write-tree-retain-branch' in $matutils_mode.outputs_extract and 'write-tree' not in $matutils_mode.outputs_extract
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	74 --write-tree tree_newick_retain_branch.nh --retain-branch-length
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	75 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	76
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	77 #elif $matutils_mode.options_mode == 'summary'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	78 #if 'samples' in $matutils_mode.summary_options
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	79 --samples samples_stats.tabular
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	80 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	81 #if 'clades' in $matutils_mode.summary_options
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	82 --clades clades_stats.tabular
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	83 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	84 #if 'sample_clades' in $matutils_mode.summary_options
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	85 --sample-clades sampleclades_stats.tabular
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	86 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	87 #if 'mutations' in $matutils_mode.summary_options
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	88 --mutations mutations_stats.tabular
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	89 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	90 #if 'aberrant' in $matutils_mode.summary_options
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	91 --aberrant aberrant_stats.tabular
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	92 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	93 #if 'haplotype' in $matutils_mode.summary_options
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	94 --haplotype haplotype_stats.tabular
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	95 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	96 #if 'calculate_roho' in $matutils_mode.summary_options
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	97 --calculate-roho roho_stats.tabular
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	98 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	99 #if 'node_stats' in $matutils_mode.summary_options
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	100 --node-stats node_stats.tabular
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	101 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	102 --output-directory ./
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	103
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	104 #elif $matutils_mode.options_mode == 'annotate'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	105 #if $matutils_mode.clade_names
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	106 --clade-names '${matutils_mode.clade_names}'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	107 #if $matutils_mode.allele_frequency
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	108 --allele-frequency $matutils_mode.allele_frequency
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	109 #end if
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	110 #if $matutils_mode.set_overlap
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	111 --set-overlap $matutils_mode.set_overlap
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	112 #end if
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	113 #if $matutils_mode.mask_frequency
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	114 --mask-frequency $matutils_mode.mask_frequency
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	115 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	116 #if $matutils_mode.clip_sample_frequency
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	117 --clip-sample-frequency $matutils_mode.clip_sample_frequency
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	118 #end if
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	119 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	120 #if $matutils_mode.clade_to_nid
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	121 --clade-to-nid '${matutils_mode.clade_to_nid}'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	122 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	123 $matutils_mode.clear_current
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	124 --output-mat output_mat.pb ##$output_mat
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	125
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	126 #elif $matutils_mode.options_mode == 'uncertainty'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	127 --samples '${matutils_mode.samples}'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	128 #if 'find-epps' in $matutils_mode.uncertainty_options
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	129 --find-epps equally_parsimonious.tabular
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	130 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	131 #if 'record-placements' in $matutils_mode.uncertainty_options
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	132 --record-placements parent_placements.tabular
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	133 #end if
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	134
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	135 #elif $matutils_mode.options_mode == 'mask'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	136 #if $matutils_mode.restricted_samples
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	137 --restricted-samples '${matutils_mode.restricted_samples}'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	138 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	139 #if $matutils_mode.rename_samples
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	140 --rename-samples '${matutils_mode.rename_samples}'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	141 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	142 #if $matutils_mode.mask_mutations
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	143 --mask-mutations '${matutils_mode.mask_mutations}'
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	144 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	145 $matutils_mode.simplify
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	146 $matutils_mode.condense_tree
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	147 --output-mat output_mat.pb ##$output_mat
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	148 #end if
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	149
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	150 --threads \${GALAXY_SLOTS:-1} > output_stdout.txt
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	151
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	152 ]]> </command>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	153 <inputs>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	154 <param name="mutation_annotation_file" type="data" format="protobuf3" label="Mutation-annotated tree object" help="Load a mutation annotated tree file, in protocol-buffers format (protobuf3)."/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	155 <conditional name="matutils_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	156 <param name="options_mode" type="select" label="matUtils mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	157 <option value="extract">Extract: subsetting and converting a MAT pb to other file formats</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	158 <option value="summary">Summary: get basic statistics and attribute information about the MAT</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	159 <option value="annotate">Annotate: adding clade annotation information to the MAT</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	160 <option value="uncertainty">Uncertainty: calculates two specific metrics for sample placement certainty</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	161 <option value="mask">Mask: mask specific samples out of the MAT, removing their mutations from visibility</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	162 </param>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	163 <when value="extract">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	164 <conditional name="operation_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	165 <param name="operation" type="select" label="Operation mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	166 <option value="samples">Select samples by naming them</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	167 <option value="clade">Select samples by clade(s)</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	168 <option value="mutation">Select samples by mutation</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	169 <option value="max-epps">Select samples by parsimonious placements</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	170 <option value="max-parsimony">Select samples by parsimonious score</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	171 <option value="nearest-k">Select samples by sample and context</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	172 <option value="max-branch-length">Remove samples by branch length</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	173 </param>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	174 <when value="samples">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	175 <param argument="--samples" type="data" format="txt" optional="True" label="Select samples by explicitly naming them, one per line in a plain text file" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	176 <param argument="--prune" type="boolean" truevalue="--prune" falsevalue="" label="Remove the selected samples" help="Remove the selected samples instead of keeping them in the output files" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	177 </when>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	178 <when value="clade">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	179 <param argument="--clade" type="text" value="" label="Select samples by membership in any of the indicated clade(s), comma delimited- e.g. -c clade1,clade2">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	180 <expand macro="sanitize_string" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	181 </param>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	182 <param argument="--prune" type="boolean" truevalue="--prune" falsevalue="" label="Remove the selected samples" help="Remove the selected samples instead of keeping them in the output files" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	183 </when>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	184 <when value="mutation">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	185 <param argument="--mutation" type="text" value="" label="Select samples by whether they contain any of the indicated mutation(s), comma delimited- e.g. -m mutation1,mutation2">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	186 <expand macro="sanitize_string" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	187 </param>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	188 <param argument="--prune" type="boolean" truevalue="--prune" falsevalue="" label="Remove the selected samples" help="Remove the selected samples instead of keeping them in the output files" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	189 </when>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	190 <when value="max-epps">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	191 <param argument="--max-epps" type="integer" min="0" max="1000" value="" label="Select samples by whether they have less than or equal to the maximum number of indicated equally parsimonious placements" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	192 <param argument="--prune" type="boolean" truevalue="--prune" falsevalue="" label="Remove the selected samples" help="Remove the selected samples instead of keeping them in the output files" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	193 </when>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	194 <when value="max-parsimony">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	195 <param argument="--max-parsimony" type="integer" min="0" max="1000" value="" label="Select samples by whether they have less than or equal to the indicated maximum parsimony score (terminal branch length)" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	196 <param argument="--prune" type="boolean" truevalue="--prune" falsevalue="" label="Remove the selected samples" help="Remove the selected samples instead of keeping them in the output files" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	197 </when>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	198 <when value="nearest-k">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	199 <param argument="--nearest-k" type="text" value="" label="Select a specific sample and X context samples, formatted as 'sample_name:X'">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	200 <expand macro="sanitize_string" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	201 </param>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	202 <param argument="--prune" type="boolean" truevalue="--prune" falsevalue="" label="Remove the selected samples" help="Remove the selected samples instead of keeping them in the output files" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	203 </when>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	204 <when value="max-branch-length">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	205 <param argument="--max-branch-length" type="integer" min="0" max="1000" value="" label="Remove samples which have branches of greater than the indicated length in their ancestry" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	206 </when>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	207 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	208 <param argument="--get-representative" type="boolean" truevalue="--get-representative" falsevalue="" label="Select two representative samples per clade" help=" Toggle to automatically select two representative samples per clade currently included in the tree, pruning all other samples from the tree. Applies after other selection steps" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	209 <param argument="--resolve-polytomies" type="boolean" truevalue="--resolve-polytomies" falsevalue="" label="Resolve all polytomies" help="Resolve all polytomies by assigning branch length 0 relationships arbitrarily. Applied after selection; prevents recondensing of the MAT" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	210 <param name="outputs_extract" type="select" display="checkboxes" multiple="true" label="Select the desired output">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	211 <option value="used-samples">Write a simple text file containing selected sample names (--used-samples)</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	212 <option value="sample-paths">Write the path of mutations defining each sample in the subtree (--sample-paths)</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	213 <option value="clade-paths">Write the path of mutations defining each clade in the subtree (--clade-paths)</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	214 <option value="all-paths">Write mutations assigned to each node in the subtree in depth-first traversal order (--all-paths)</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	215 <option value="write-vcf">Output VCF file representing selected subtree (--write-vcf)</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	216 <option value="write-vcf-no-genotypes">Output VCF file representing selected subtree without including genotype column (--write-vcf --no-genotypes) </option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	217 <option value="write-mat">Write the selected subtree as a mutation annotated tree (--write-math)</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	218 <option value="write-mat-collapsed">Write the selected subtree as a collapsed mutation annotated tree (--write-mat --collapsed)</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	219 <option value="write-json">Write an Auspice-compatbile json representing the selected subtree (--write-json)</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	220 <option value="write-tree"> Write a newick string representing the selected subtree (--write-tree)</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	221 <option value="write-tree-retain-branch"> Write a newick string representing the selected subtree without recalculating branch lengths (--write-tree --retain-branch)</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	222 </param>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	223 </when>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	224 <when value="summary">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	225 <param name="summary_options" type="select" display="checkboxes" multiple="true" label="Select statistics and attribute information">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	226 <option value="general">Number of nodes, number of samples, number of condensed nodes, and total tree parsimony</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	227 <option value="samples">Samples in the tree and their parsimony score (--samples)</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	228 <option value="clades">Clades and the count of associated samples in the tree (--clades)</option>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	229 <option value="sample_clades">All samples and their associated clade values (--sample-clades)</option>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	230 <option value="mutations">Mutations in the tree and their occurrence count (--mutations)</option>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	231 <option value="aberrant">Potentially problematic nodes (--aberrant)</option>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	232 <option value="haplotype">Haplotypes and their total frequency (--haplotype)</option>
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	233 <option value="calculate_roho">Distribution of RoHO values for all homoplasic mutations (--calculate-roho)</option>
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	234 <option value="node_stats">Per internal node, the number of descendents, mutations, mutational density, and reversion mutations (--node-stats)</option>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	235 </param>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	236 </when>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	237 <when value="annotate">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	238 <param argument="--clade-names" type="data" format="tabular" optional="True" label="File containing clade asssignments of samples" help="An algorithm automatically locates and annotates clade root nodes."/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	239 <param argument="--clade-to-nid" type="data" format="tabular" optional="True" label="File mapping clades to their respective internal node identifiers" help="Internal node names are not maintained when saving and loading from a .pb file. It is not guaranteed that internal node names will correspond directly between two .pb files, so use the direct assignment method with caution."/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	240 <param argument="--set-overlap" type="float" min="0" max="1" value="" optional="True" label="Minimum fraction of the lineage samples" help="Minimum fraction of the lineage samples that should be desecendants of the assigned clade root. Used only with --clade-names" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	241 <param argument="--clear-current" type="boolean" truevalue="--clear-current" falsevalue="" label="Remove current annotations" help="Use to remove current annotations before applying new annotations." />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	242 <param argument="--allele-frequency" type="float" min="0" max="1" value="" optional="True" label="Minimum allele frequency for finding the best clade root" help="Minimum allele frequency in input samples for finding the best clade root. Used only with 'remove current annotation'. Used only with --clade-names" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	243 <param argument="--mask-frequency" type="float" min="0" max="1" value="" optional="True" label="Minimum allele frequency for being masked" help="Minimum allele frequency in input samples that should be masked for finding the best clade root. Used only with --clade-names" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	244 <param argument="--clip-sample-frequency" type="float" min="0" max="1" value="" optional="True" label="Clip sample frequency" help="Maximum proportion of samples in a branch that are exemplars from --clade-names to consider when sorting candidate clade root nodes." />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	245 </when>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	246 <when value="uncertainty">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	247 <param argument="--samples" type="data" format="txt" label="Select samples by explicitly naming them, one per line in a plain text file" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	248 <param name="uncertainty_options" type="select" display="checkboxes" multiple="true" label="Metrics for sample placement certainty">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	249 <option value="find-epps">Number of equally parsimonious placements for each sample (--find-epps)</option>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	250 <option value="record-placements">Record potential parents for each sample (--record-placements)</option>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	251 </param>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	252 </when>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	253 <when value="mask">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	254 <param argument="--restricted-samples" type="data" format="txt" optional="True" label="Select samples by explicitly naming them, one per line in a plain text file" help="Sample names to restrict. Use to perform masking"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	255 <param argument="--rename-samples" type="data" format="tabular" optional="True" label="TSV file containing names of the samples to be renamed and their new names"/>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	256 <param argument="--mask-mutations" type="data" format="tabular" optional="True" label="TSV or CSV containing mutations to be masked in the first column and locations to mask downstream from in the second."/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	257 <param argument="--simplify" type="boolean" truevalue="--simplify" falsevalue="" label="Use to automatically remove identifying information from the tree, including all sample names and private mutations" />
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	258 <param argument="--condense-tree" type="boolean" truevalue="--condense-tree" falsevalue="" label="Use to recondense the tree before saving." />
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	259 </when>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	260 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	261 </inputs>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	262 <outputs>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	263 <data name="selected_samples" format="txt" from_work_dir='selected_samples.txt' label="${tool.name} on ${on_string}: selected samples">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	264 <filter>matutils_mode['options_mode'] == 'extract' and 'used-samples' in matutils_mode['outputs_extract'] </filter>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	265 </data>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	266 <data name="path_mutations" format="tabular" from_work_dir='path_mutations.tabular' label="${tool.name} on ${on_string}: sample mutations">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	267 <filter>matutils_mode['options_mode'] == 'extract' and 'sample-paths' in matutils_mode['outputs_extract']</filter>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	268 </data>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	269 <data name="path_clades" format="tabular" from_work_dir='path_clades.tabular' label="${tool.name} on ${on_string}: clade mutations">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	270 <filter>matutils_mode['options_mode'] == 'extract' and 'clade-paths' in matutils_mode['outputs_extract']</filter>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	271 </data>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	272 <data name="all_paths" format="txt" from_work_dir='all_paths.txt' label="${tool.name} on ${on_string}: node mutations">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	273 <filter>matutils_mode['options_mode'] == 'extract' and 'all-paths' in matutils_mode['outputs_extract']</filter>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	274 </data>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	275 <data name="subtree_vcf" format="vcf" from_work_dir='subtree_vcf.vcf' label="${tool.name} on ${on_string}: subtree">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	276 <filter>matutils_mode['options_mode'] == 'extract' and 'write-vcf' in matutils_mode['outputs_extract']</filter>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	277 </data>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	278 <data name="subtree_no_genotype_vcf" format="vcf" from_work_dir='subtree_vcf_no_genotypes.vcf' label="${tool.name} on ${on_string}: subtree without genotype">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	279 <filter>matutils_mode['options_mode'] == 'extract' and 'write-vcf-no-genotypes' in matutils_mode['outputs_extract'] and 'write-vcf' not in matutils_mode['outputs_extract']</filter>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	280 </data>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	281 <data name="mutation_annotated" format="protobuf3" from_work_dir='mutation_annotated.pb' label="${tool.name} on ${on_string}: mutation annotated tree">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	282 <filter>matutils_mode['options_mode'] == 'extract' and 'write-mat' in matutils_mode['outputs_extract'] </filter>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	283 </data>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	284 <data name="mutation_annotated_collapsed" format="protobuf3" from_work_dir='mutation_annotated_collapsed.pb' label="${tool.name} on ${on_string}: mutation annotated tree collapsed">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	285 <filter>matutils_mode['options_mode'] == 'extract' and 'write-mat-collapse' in matutils_mode['outputs_extract'] and 'write-mat' not in matutils_mode['outputs_extract']</filter>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	286 </data>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	287 <data name="subtree_json" format="json" from_work_dir='subtree_json.json' label="${tool.name} on ${on_string}: subtree (json)">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	288 <filter>matutils_mode['options_mode'] == 'extract' and 'write-json' in matutils_mode['outputs_extract']</filter>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	289 </data>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	290 <data name="tree_newick" format="newick" from_work_dir='tree_newick.nh' label="${tool.name} on ${on_string}: subtree (newick)">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	291 <filter>matutils_mode['options_mode'] == 'extract' and 'write-tree' in matutils_mode['outputs_extract']</filter>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	292 </data>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	293 <data name="tree_newick_retain_branch" format="newick" from_work_dir='tree_newick_retain_branch.nh' label="${tool.name} on ${on_string}: subtree retain branch (newick)">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	294 <filter>matutils_mode['options_mode'] == 'extract' and 'write-tree-retain-branch' in matutils_mode['outputs_extract'] and 'write-tree' not in matutils_mode['outputs_extract']</filter>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	295 </data>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	296 <data name="general_stats" format="txt" from_work_dir='output_stdout.txt' label="${tool.name} on ${on_string}: general stats">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	297 <filter>matutils_mode['options_mode'] == 'summary' and 'general' in matutils_mode['summary_options']</filter>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	298 </data>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	299 <data name="samples_stats" format="tabular" from_work_dir='samples_stats.tabular' label="${tool.name} on ${on_string}: samples stats">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	300 <filter>matutils_mode['options_mode'] == 'summary' and 'samples' in matutils_mode['summary_options']</filter>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	301 </data>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	302 <data name="clades_stats" format="tabular" from_work_dir='clades_stats.tabular' label="${tool.name} on ${on_string}: clades stats">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	303 <filter>matutils_mode['options_mode'] == 'summary' and 'clades' in matutils_mode['summary_options']</filter>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	304 </data>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	305 <data name="sampleclades_stats" format="tabular" from_work_dir='sampleclades_stats.tabular' label="${tool.name} on ${on_string}: sample - clades stats">
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	306 <filter>matutils_mode['options_mode'] == 'summary' and 'sample_clades' in matutils_mode['summary_options']</filter>
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	307 </data>
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	308
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	309 <data name="mutations_stats" format="tabular" from_work_dir='mutations_stats.tabular' label="${tool.name} on ${on_string}: mutations stats">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	310 <filter>matutils_mode['options_mode'] == 'summary' and 'mutations' in matutils_mode['summary_options']</filter>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	311 </data>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	312 <data name="aberrant_stats" format="tabular" from_work_dir='aberrant_stats.tabular' label="${tool.name} on ${on_string}: aberrant stats">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	313 <filter>matutils_mode['options_mode'] == 'summary' and 'aberrant' in matutils_mode['summary_options']</filter>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	314 </data>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	315 <data name="haplotype_stats" format="tabular" from_work_dir='haplotype_stats.tabular' label="${tool.name} on ${on_string}: haplotype stats">
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	316 <filter>matutils_mode['options_mode'] == 'summary' and 'haplotype' in matutils_mode['summary_options']</filter>
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	317 </data>
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	318 <data name="roho_stats" format="tabular" from_work_dir='roho_stats.tabular' label="${tool.name} on ${on_string}: RoHo stats">
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	319 <filter>matutils_mode['options_mode'] == 'summary' and 'calculate_roho' in matutils_mode['summary_options']</filter>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	320 </data>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	321 <data name="node_stats" format="tabular" from_work_dir='node_stats.tabular' label="${tool.name} on ${on_string}: node stats">
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	322 <filter>matutils_mode['options_mode'] == 'summary' and 'node_stats' in matutils_mode['summary_options']</filter>
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	323 </data>
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	324 <data name="output_mat" format="protobuf3" from_work_dir='output_mat.pb' label="${tool.name} on ${on_string}: mutation tree">
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	325 <filter>matutils_mode['options_mode'] == 'annotate' or matutils_mode['options_mode'] == 'mask'</filter>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	326 </data>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	327 <data name="equally_parsimonious" from_work_dir='equally_parsimonious.tabular' format="tabular" label="${tool.name} on ${on_string}: equally parsimonious placements">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	328 <filter>matutils_mode['options_mode'] == 'uncertainty' and 'find-epps' in matutils_mode['uncertainty_options']</filter>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	329 </data>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	330 <data name="parent_placements" format="tabular" from_work_dir='parent_placements.tabular' label="${tool.name} on ${on_string}: Potential parents">
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	331 <filter>matutils_mode['options_mode'] == 'uncertainty' and 'record-placements' in matutils_mode['uncertainty_options']</filter>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	332 </data>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	333 </outputs>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	334 <tests>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	335 <test expect_num_outputs="3">
1 75e51e947a98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79" iuc parents: 0 diff changeset	336 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	337 <conditional name="matutils_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	338 <param name="options_mode" value="extract"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	339 <param name="resolve_polytomies" value="true"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	340 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	341 <conditional name="operation_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	342 <param name="operation" value="samples"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	343 <param name="samples" value="sample_names.txt"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	344 <param name="prune" value="true"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	345 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	346 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	347 <output name="selected_samples" file="test_13_sample_names.txt" ftype="txt"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	348 <output name="path_mutations" file="test_13_path_mutations.tabular" ftype="tabular"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	349 <output name="path_clades" file="test_13_path_clades.tabular" ftype="tabular"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	350 </test>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	351 <test expect_num_outputs="5">
1 75e51e947a98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79" iuc parents: 0 diff changeset	352 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	353 <conditional name="matutils_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	354 <param name="options_mode" value="extract"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	355 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	356 <conditional name="operation_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	357 <param name="operation" value="samples"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	358 <param name="samples" value="sample_names.txt"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	359 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	360 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	361 <output name="selected_samples" file="test_14_sample_names.txt" ftype="txt"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	362 <output name="path_mutations" file="test_14_path_mutations.tabular" ftype="tabular"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	363 <output name="path_clades" file="test_14_path_clades.tabular" ftype="tabular"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	364 <output name="all_paths" file="test_14_all_paths.txt" ftype="txt"/>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	365 <output name="subtree_vcf" ftype="vcf" >
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	366 <assert_contents>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	367 <has_line line="##fileformat=VCFv4.2" />
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	368 <has_line_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT.+" />
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	369 <has_n_columns n="1105" comment="#" />
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	370 <has_n_lines n="3204" />
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	371 </assert_contents>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	372 </output>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	373 </test>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	374 <test expect_num_outputs="4">
1 75e51e947a98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79" iuc parents: 0 diff changeset	375 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	376 <conditional name="matutils_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	377 <param name="options_mode" value="extract"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	378 <param name="outputs_extract" value="write-vcf-no-genotypes,write-mat,write-json,write-tree"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	379 <conditional name="operation_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	380 <param name="operation" value="mutation"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	381 <param name="mutation" value="C241T"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	382 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	383 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	384 <output name="subtree_no_genotype_vcf" file="test_15_subtree_no_genotype.vcf" ftype="vcf"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	385 <output name="mutation_annotated" file="test_15_mutation_annotated_tree.pb" ftype="protobuf3"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	386 <output name="subtree_json" file="test_15_subtree.json" ftype="json"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	387 <output name="tree_newick" file="test_15_tree.nh" ftype="newick"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	388 </test>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	389 <test expect_num_outputs="3">
1 75e51e947a98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79" iuc parents: 0 diff changeset	390 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	391 <conditional name="matutils_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	392 <param name="options_mode" value="extract"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	393 <param name="outputs_extract" value="used-samples,sample-paths,write-vcf"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	394 <conditional name="operation_mode">
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	395 <param name="operation" value="clade"/>
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	396 <param name="clade" value="B.1.160.7,B.1.258.4"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	397 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	398 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	399 <output name="selected_samples" file="test_16_sample_names.txt" ftype="txt"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	400 <output name="path_mutations" file="test_16_path_mutations.tabular" ftype="tabular"/>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	401 <output name="subtree_vcf" file="test_16_subtree.vcf" ftype="vcf" />
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	402 </test>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	403 <test expect_num_outputs="5">
1 75e51e947a98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79" iuc parents: 0 diff changeset	404 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	405 <conditional name="matutils_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	406 <param name="options_mode" value="extract"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	407 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	408 <conditional name="operation_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	409 <param name="operation" value="max-epps"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	410 <param name="max_epps" value="0"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	411 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	412 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	413 <output name="selected_samples" file="test_17_sample_names.txt" ftype="txt"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	414 <output name="path_mutations" file="test_17_path_mutations.tabular" ftype="tabular"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	415 <output name="path_clades" file="test_17_path_clades.tabular" ftype="tabular"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	416 <output name="all_paths" file="test_17_all_paths.txt" ftype="txt"/>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	417 <output name="subtree_vcf" ftype="vcf" >
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	418 <assert_contents>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	419 <has_line line="##fileformat=VCFv4.2" />
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	420 <has_line_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT.+" />
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	421 <has_n_columns n="1243" comment="#" />
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	422 <has_n_lines n="3558" />
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	423 </assert_contents>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	424 </output>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	425 </test>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	426 <test expect_num_outputs="5">
1 75e51e947a98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79" iuc parents: 0 diff changeset	427 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	428 <conditional name="matutils_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	429 <param name="options_mode" value="extract"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	430 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	431 <conditional name="operation_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	432 <param name="operation" value="max-parsimony"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	433 <param name="max_parsimony" value="1"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	434 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	435 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	436 <output name="selected_samples" file="test_18_sample_names.txt" ftype="txt"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	437 <output name="path_mutations" file="test_18_path_mutations.tabular" ftype="tabular"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	438 <output name="path_clades" file="test_18_path_clades.tabular" ftype="tabular"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	439 <output name="all_paths" file="test_18_all_paths.txt" ftype="txt"/>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	440 <output name="subtree_vcf" ftype="vcf" >
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	441 <assert_contents>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	442 <has_line line="##fileformat=VCFv4.2" />
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	443 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT.+" />
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	444 <has_n_columns n="450" comment="#" />
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	445 <has_n_lines n="1256" />
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	446 </assert_contents>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	447 </output>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	448 </test>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	449 <test expect_num_outputs="3">
1 75e51e947a98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79" iuc parents: 0 diff changeset	450 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	451 <conditional name="matutils_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	452 <param name="options_mode" value="extract"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	453 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	454 <conditional name="operation_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	455 <param name="operation" value="max-branch-length"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	456 <param name="max_branch_length" value="2"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	457 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	458 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	459 <output name="selected_samples" file="test_19_sample_names.txt" ftype="txt"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	460 <output name="path_mutations" file="test_19_path_mutations.tabular" ftype="tabular"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	461 <output name="path_clades" file="test_19_path_clades.tabular" ftype="tabular"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	462 </test>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	463 <test expect_num_outputs="1">
1 75e51e947a98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79" iuc parents: 0 diff changeset	464 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	465 <conditional name="matutils_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	466 <param name="options_mode" value="summary"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	467 <param name="summary_options" value="general"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	468 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	469 <output name="general_stats" file="test_20_general_stats.txt" ftype="txt"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	470 </test>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	471 <test expect_num_outputs="8">
1 75e51e947a98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79" iuc parents: 0 diff changeset	472 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	473 <conditional name="matutils_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	474 <param name="options_mode" value="summary"/>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	475 <param name="summary_options" value="samples,clades,mutations,aberrant,sample_clades,haplotype,calculate_roho,node_stats"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	476 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	477 <output name="samples_stats" file="test_21_sample_stats.tabular" ftype="tabular"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	478 <output name="clades_stats" file="test_21_clades_stats.tabular" ftype="tabular"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	479 <output name="mutations_stats" file="test_21_mutations_stats.tabular" ftype="tabular"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	480 <output name="aberrant_stats" file="test_21_aberrant_stats.tabular" ftype="tabular"/>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	481 <output name="sampleclades_stats" file="test_21_sampleclades_stats.tabular" ftype="tabular"/>
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	482 <output name="haplotype_stats" file="test_21_haplotype_stats.tabular" ftype="tabular"/>
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	483 <output name="roho_stats" file="test_21_roho_stats.tabular" ftype="tabular"/>
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	484 <output name="node_stats" file="test_21_node_stats.tabular" ftype="tabular"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	485 </test>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	486 <test expect_num_outputs="1">
1 75e51e947a98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79" iuc parents: 0 diff changeset	487 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	488 <conditional name="matutils_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	489 <param name="options_mode" value="uncertainty"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	490 <param name="samples" value="sample_names.txt"/>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	491 <param name="uncertainty_options" value="record-placements"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	492 </conditional>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	493 <output name="parent_placements" ftype="tabular" >
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	494 <assert_contents>
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	495 <has_line_matching expression="placement\tsample" />
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	496 <has_n_columns n="2" />
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	497 <has_n_lines n="3240" />
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	498 </assert_contents>
daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	499 </output>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	500 </test>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	501 <test expect_num_outputs="1">
1 75e51e947a98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79" iuc parents: 0 diff changeset	502 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	503 <conditional name="matutils_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	504 <param name="options_mode" value="uncertainty"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	505 <param name="samples" value="sample_names.txt"/>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	506 <param name="uncertainty_options" value="find-epps"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	507 </conditional>
2 daa704d3ac8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd iuc parents: 1 diff changeset	508 <output name="equally_parsimonious" file="test_23_equally_parsimonious.tabular" ftype="tabular"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	509 </test>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	510 <test expect_num_outputs="1">
1 75e51e947a98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79" iuc parents: 0 diff changeset	511 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	512 <conditional name="matutils_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	513 <param name="options_mode" value="mask"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	514 <param name="restricted_samples" value="sample_names.txt"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	515 <param name="simplify" value="true"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	516 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	517 <output name="output_mat" file="test_24_restricted.pb" ftype="protobuf3"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	518 </test>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	519 <test expect_num_outputs="1">
1 75e51e947a98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79" iuc parents: 0 diff changeset	520 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0 be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	521 <conditional name="matutils_mode">
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	522 <param name="options_mode" value="mask"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	523 <param name="rename_samples" value="rename_samples.tabular"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	524 </conditional>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	525 <output name="output_mat" file="test_25_renamed.pb" ftype="protobuf3"/>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	526 </test>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	527 </tests>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	528 <help><![CDATA[
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	529
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	530 .. class:: infomark
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	531
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	532 Purpose
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	533
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	534 matUtils is a suite of tools used to analyze, edit, and manipulate mutation annotated tree (.pb) files.
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	535
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	536 ----
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	537
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	538 .. class:: infomark
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	539
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	540 matUtils Common Options
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	541
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	542 Extract: matUtils extract serves as a flexible prebuilt pipeline, and serves as the primary tool for subsetting and converting a MAT pb to other file formats.
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	543 Sumary: matUtils summary is used to get basic statistics and attribute information about the mat.
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	544 Annotate: matUtils annotate is a function for adding clade annotation information to the pb.
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	545 Uncertainly: matUtils uncertainty calculates two specific metrics for sample placement certainty. These metrics can be very important to support contact tracing and reliable identification of the origin of a newly placed sample.
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	546 Mask: matUtils mask is used to mask specific samples out of the pb, removing their mutations from visibility.
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	547
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	548 You can find more information in the `matUtils official documentation page <https://usher-wiki.readthedocs.io/en/latest/matUtils.html>`_.
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	549
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	550 ]]> </help>
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	551 <expand macro="citations" />
be59fa64e855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	552 </tool>

Mercurial > repos > iuc > usher_matutils

annotate matutils.xml @ 2:daa704d3ac8f draft default tip