annotate matutils.xml @ 2:e0a0a473fc1e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 5de7b91f2bda9c351f9512601f899248b7278924
author iuc
date Sun, 17 Mar 2024 18:10:36 +0000
parents 52fd1d491417
children
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1 <tool id='usher_matutils' name='UShER matUtils' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.01'>
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2 <description>analyze, edit, and manipulate mutation annotated tree files</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
2
e0a0a473fc1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 5de7b91f2bda9c351f9512601f899248b7278924
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6 <expand macro="xrefs"/>
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7 <expand macro='requirements' />
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8 <version_command>usher --version</version_command>
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9 <command detect_errors='exit_code'><![CDATA[
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10 matUtils
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11 $matutils_mode.options_mode
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12 --input-mat $mutation_annotation_file
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13 #if $matutils_mode.options_mode == 'extract'
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14 #if $matutils_mode.operation_mode.operation == 'samples'
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15 #if $matutils_mode.operation_mode.samples
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16 --samples '${matutils_mode.operation_mode.samples}'
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17 #end if
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18 $matutils_mode.operation_mode.prune
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19 #elif $matutils_mode.operation_mode.operation == 'clade'
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20 --clade '${matutils_mode.operation_mode.clade}'
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21 $matutils_mode.operation_mode.prune
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22 #elif $matutils_mode.operation_mode.operation == 'mutation'
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23 --mutation '${matutils_mode.operation_mode.mutation}'
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24 $matutils_mode.operation_mode.prune
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25 #elif $matutils_mode.operation_mode.operation == 'max-epps'
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26 --max-epps $matutils_mode.operation_mode.max_epps
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27 $matutils_mode.operation_mode.prune
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28 #elif $matutils_mode.operation_mode.operation == 'max-parsimony'
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29 --max-parsimony $matutils_mode.operation_mode.max_parsimony
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30 $matutils_mode.operation_mode.prune
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31 #elif $matutils_mode.operation_mode.operation == 'nearest-k'
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32 --nearest-k '${matutils_mode.operation_mode.nearest_k}'
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33 $matutils_mode.operation_mode.prune
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34 #elif $matutils_mode.operation_mode.operation == 'max-branch-length'
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35 --max-branch-length $matutils_mode.operation_mode.max_branch_length
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36 #end if
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37 $matutils_mode.get_representative
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38 $matutils_mode.resolve_polytomies
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39 #if 'used-samples' in $matutils_mode.outputs_extract
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40 --used-samples selected_samples.txt ##$selected_samples
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41 #end if
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42 #if 'sample-paths' in $matutils_mode.outputs_extract
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43 --sample-paths path_mutations.tabular ##$path_mutations
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44 #end if
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45 #if 'clade-paths' in $matutils_mode.outputs_extract
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46 --clade-paths path_clades.tabular ##$path_clades
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47 #end if
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48 #if 'all-paths' in $matutils_mode.outputs_extract
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49 --all-paths all_paths.txt ##$all_paths
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50 #end if
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51 #if 'write-vcf' in $matutils_mode.outputs_extract
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52 --write-vcf subtree_vcf.vcf ##$subtree_vcf
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53 #end if
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54 #if 'write-vcf-no-genotypes' in $matutils_mode.outputs_extract and 'write-vcf' not in $matutils_mode.outputs_extract
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55 --write-vcf subtree_vcf_no_genotypes.vcf --no-genotypes
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56 #end if
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57 #if 'write-mat' in $matutils_mode.outputs_extract
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58 --write-mat mutation_annotated.pb ##$mutation_annotated
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59 #end if
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60 #if 'write-mat-collapsed' in $matutils_mode.outputs_extract and 'write-mat' not in $matutils_mode.outputs_extract
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61 --write-mat mutation_annotated_collapsed.pb --collapsed-tree
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62 #end if
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63 #if 'write-json' in $matutils_mode.outputs_extract
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64 --write-json subtree_json.json ##$subtree_json
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65 #end if
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66 #if 'write-tree' in $matutils_mode.outputs_extract
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67 --write-tree tree_newick.nh ##$tree_newick
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68 #end if
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69 #if 'write-tree-retain-branch' in $matutils_mode.outputs_extract and 'write-tree' not in $matutils_mode.outputs_extract
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70 --write-tree tree_newick_retain_branch.nh --retain-branch-length
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71 #end if
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72 #elif $matutils_mode.options_mode == 'summary'
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73 #if 'samples' in $matutils_mode.summary_options
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74 --samples samples_stats.tabular
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75 #end if
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76 #if 'clades' in $matutils_mode.summary_options
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77 --clades clades_stats.tabular
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78 #end if
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79 #if 'mutations' in $matutils_mode.summary_options
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80 --mutations mutations_stats.tabular
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81 #end if
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82 #if 'aberrant' in $matutils_mode.summary_options
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83 --aberrant aberrant_stats.tabular
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84 #end if
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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85 --output-directory ./
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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86 #elif $matutils_mode.options_mode == 'annotate'
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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87 #if $matutils_mode.clade_names
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88 --clade-names '${matutils_mode.clade_names}'
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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89 #if $matutils_mode.allele_frequency
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90 --allele-frequency $matutils_mode.allele_frequency
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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91 #end if
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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92 #if $matutils_mode.set_overlap
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93 --set-overlap $matutils_mode.set_overlap
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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94 #end if
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95 #if $matutils_mode.mask_frequency
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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96 --mask-frequency $matutils_mode.mask_frequency
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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97 #end if
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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98 #if $matutils_mode.clip_sample_frequency
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99 --clip-sample-frequency $matutils_mode.clip_sample_frequency
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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100 #end if
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101 #end if
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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102 #if $matutils_mode.clade_to_nid
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103 --clade-to-nid '${matutils_mode.clade_to_nid}'
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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104 #end if
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105 $matutils_mode.clear_current
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106 --output-mat output_mat.pb ##$output_mat
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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107 #elif $matutils_mode.options_mode == 'uncertainty'
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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108 --samples '${matutils_mode.samples}'
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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109 #if 'get-parsimony' in $matutils_mode.uncertainty_options
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110 --get-parsimony
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111 #end if
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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112 #if 'find-epps' in $matutils_mode.uncertainty_options
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113 --find-epps equally_parsimonious.tabular
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114 #end if
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115 #if 'find-neighborhood' in $matutils_mode.uncertainty_options
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116 --find-neighborhood neighborhood.tabular
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117 #end if
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118 #elif $matutils_mode.options_mode == 'mask'
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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119 #if $matutils_mode.restricted_samples
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120 --restricted-samples '${matutils_mode.restricted_samples}'
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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121 #end if
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122 #if $matutils_mode.rename_samples
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123 --rename-samples '${matutils_mode.rename_samples}'
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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124 #end if
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125 $$matutils_mode.simplify
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126 --output-mat output_mat.pb ##$output_mat
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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127 #end if
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128 --threads \${GALAXY_SLOTS:-1} > output_stdout.txt
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129
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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130 ]]> </command>
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131 <inputs>
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132 <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)."/>
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133 <conditional name="matutils_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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134 <param name="options_mode" type="select" label="matUtils mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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135 <option value="extract">Extract: subsetting and converting a MAT pb to other file formats</option>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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136 <option value="summary">Summary: get basic statistics and attribute information about the MAT</option>
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137 <option value="annotate">Annotate: adding clade annotation information to the MAT</option>
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138 <option value="uncertainty">Uncertainty: calculates two specific metrics for sample placement certainty</option>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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139 <option value="mask">Mask: mask specific samples out of the MAT, removing their mutations from visibility</option>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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140 </param>
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141 <when value="extract">
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142 <conditional name="operation_mode">
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143 <param name="operation" type="select" label="Operation mode">
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144 <option value="samples">Select samples by naming them</option>
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145 <option value="clade">Select samples by clade(s)</option>
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146 <option value="mutation">Select samples by mutation</option>
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147 <option value="max-epps">Select samples by parsimonious placements</option>
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148 <option value="max-parsimony">Select samples by parsimonious score</option>
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149 <option value="nearest-k">Select samples by sample and context</option>
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150 <option value="max-branch-length">Remove samples by branch length</option>
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151 </param>
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152 <when value="samples">
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153 <param argument="--samples" type="data" format="txt" optional="True" label="Select samples by explicitly naming them, one per line in a plain text file" />
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154 <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" />
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155 </when>
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156 <when value="clade">
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157 <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">
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158 <expand macro="sanitize_string" />
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159 </param>
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160 <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" />
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161 </when>
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162 <when value="mutation">
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163 <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">
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164 <expand macro="sanitize_string" />
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165 </param>
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166 <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" />
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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167 </when>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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168 <when value="max-epps">
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169 <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" />
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170 <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" />
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171 </when>
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172 <when value="max-parsimony">
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173 <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)" />
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174 <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" />
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175 </when>
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176 <when value="nearest-k">
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177 <param argument="--nearest-k" type="text" value="" label="Select a specific sample and X context samples, formatted as 'sample_name:X'">
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178 <expand macro="sanitize_string" />
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179 </param>
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180 <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" />
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181 </when>
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182 <when value="max-branch-length">
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183 <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" />
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184 </when>
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185 </conditional>
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186 <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" />
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187 <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" />
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188 <param name="outputs_extract" type="select" display="checkboxes" multiple="true" label="Select the desired output">
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189 <option value="used-samples">Write a simple text file containing selected sample names (--used-samples)</option>
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190 <option value="sample-paths">Write the path of mutations defining each sample in the subtree (--sample-paths)</option>
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191 <option value="clade-paths">Write the path of mutations defining each clade in the subtree (--clade-paths)</option>
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192 <option value="all-paths">Write mutations assigned to each node in the subtree in depth-first traversal order (--all-paths)</option>
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193 <option value="write-vcf">Output VCF file representing selected subtree (--write-vcf)</option>
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194 <option value="write-vcf-no-genotypes">Output VCF file representing selected subtree without including genotype column (--write-vcf --no-genotypes) </option>
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195 <option value="write-mat">Write the selected subtree as a mutation annotated tree (--write-math)</option>
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196 <option value="write-mat-collapsed">Write the selected subtree as a collapsed mutation annotated tree (--write-mat --collapsed)</option>
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197 <option value="write-json">Write an Auspice-compatbile json representing the selected subtree (--write-json)</option>
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198 <option value="write-tree"> Write a newick string representing the selected subtree (--write-tree)</option>
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199 <option value="write-tree-retain-branch"> Write a newick string representing the selected subtree without recalculating branch lengths (--write-tree --retain-branch)</option>
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200 </param>
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201 </when>
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202 <when value="summary">
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203 <param name="summary_options" type="select" display="checkboxes" multiple="true" label="Select statistics and attribute information">
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204 <option value="general">Number of nodes, number of samples, number of condensed nodes, and total tree parsimony</option>
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205 <option value="samples">Samples in the tree and their parsimony score (--samples)</option>
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206 <option value="clades">Clades and the count of associated samples in the tree (--clades)</option>
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207 <option value="mutations">Mutations in the tree and their occurrence count (--mutations)</option>
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208 <option value="aberrant">Potentially problematic nodes (--aberrant)</option>
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209 </param>
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210 </when>
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211 <when value="annotate">
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212 <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."/>
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213 <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."/>
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214 <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" />
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215 <param argument="--clear-current" type="boolean" truevalue="--clear-current" falsevalue="" label="Remove current annotations" help="Use to remove current annotations before applying new annotations." />
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216 <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" />
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217 <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" />
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218 <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." />
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219 </when>
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220 <when value="uncertainty">
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221 <param argument="--samples" type="data" format="txt" label="Select samples by explicitly naming them, one per line in a plain text file" />
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222 <param name="uncertainty_options" type="select" display="checkboxes" multiple="true" label="Metrics for sample placement certainty">
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223 <option value="get-parsimony">Total tree parsimony score (--get-parsimony)</option>
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224 <option value="find-epps">Number of equally parsimonious placements for each sample (--find-epps)</option>
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225 <option value="find-neighborhood">Neighborhood size scores (--find-neighborhood)</option>
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226 </param>
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227 </when>
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228 <when value="mask">
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229 <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"/>
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230 <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"/>
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231 <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" />
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232 </when>
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233 </conditional>
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234 </inputs>
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235 <outputs>
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236 <data name="selected_samples" format="txt" from_work_dir='selected_samples.txt' label="${tool.name} on ${on_string}: selected samples">
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237 <filter>matutils_mode['options_mode'] == 'extract' and 'used-samples' in matutils_mode['outputs_extract'] </filter>
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238 </data>
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239 <data name="path_mutations" format="tabular" from_work_dir='path_mutations.tabular' label="${tool.name} on ${on_string}: sample mutations">
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240 <filter>matutils_mode['options_mode'] == 'extract' and 'sample-paths' in matutils_mode['outputs_extract']</filter>
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241 </data>
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242 <data name="path_clades" format="tabular" from_work_dir='path_clades.tabular' label="${tool.name} on ${on_string}: clade mutations">
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243 <filter>matutils_mode['options_mode'] == 'extract' and 'clade-paths' in matutils_mode['outputs_extract']</filter>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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244 </data>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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245 <data name="all_paths" format="txt" from_work_dir='all_paths.txt' label="${tool.name} on ${on_string}: node mutations">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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246 <filter>matutils_mode['options_mode'] == 'extract' and 'all-paths' in matutils_mode['outputs_extract']</filter>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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247 </data>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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248 <data name="subtree_vcf" format="vcf" from_work_dir='subtree_vcf.vcf' label="${tool.name} on ${on_string}: subtree">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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249 <filter>matutils_mode['options_mode'] == 'extract' and 'write-vcf' in matutils_mode['outputs_extract']</filter>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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250 </data>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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251 <data name="subtree_no_genotype_vcf" format="vcf" from_work_dir='subtree_vcf_no_genotypes.vcf' label="${tool.name} on ${on_string}: subtree without genotype">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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252 <filter>matutils_mode['options_mode'] == 'extract' and 'write-vcf-no-genotypes' in matutils_mode['outputs_extract'] and 'write-vcf' not in matutils_mode['outputs_extract']</filter>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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253 </data>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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254 <data name="mutation_annotated" format="protobuf3" from_work_dir='mutation_annotated.pb' label="${tool.name} on ${on_string}: mutation annotated tree">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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255 <filter>matutils_mode['options_mode'] == 'extract' and 'write-mat' in matutils_mode['outputs_extract'] </filter>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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256 </data>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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257 <data name="mutation_annotated_collapsed" format="protobuf3" from_work_dir='mutation_annotated_collapsed.pb' label="${tool.name} on ${on_string}: mutation annotated tree collapsed">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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258 <filter>matutils_mode['options_mode'] == 'extract' and 'write-mat-collapse' in matutils_mode['outputs_extract'] and 'write-mat' not in matutils_mode['outputs_extract']</filter>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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259 </data>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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260 <data name="subtree_json" format="json" from_work_dir='subtree_json.json' label="${tool.name} on ${on_string}: subtree (json)">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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261 <filter>matutils_mode['options_mode'] == 'extract' and 'write-json' in matutils_mode['outputs_extract']</filter>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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262 </data>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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263 <data name="tree_newick" format="newick" from_work_dir='tree_newick.nh' label="${tool.name} on ${on_string}: subtree (newick)">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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264 <filter>matutils_mode['options_mode'] == 'extract' and 'write-tree' in matutils_mode['outputs_extract']</filter>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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265 </data>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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266 <data name="tree_newick_retain_branch" format="newick" from_work_dir='tree_newick_retain_branch.nh' label="${tool.name} on ${on_string}: subtree retain branch (newick)">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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267 <filter>matutils_mode['options_mode'] == 'extract' and 'write-tree-retain-branch' in matutils_mode['outputs_extract'] and 'write-tree' not in matutils_mode['outputs_extract']</filter>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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268 </data>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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269 <data name="general_stats" format="txt" from_work_dir='output_stdout.txt' label="${tool.name} on ${on_string}: general stats">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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270 <filter>matutils_mode['options_mode'] == 'summary' and 'general' in matutils_mode['summary_options']</filter>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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271 </data>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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272 <data name="samples_stats" format="tabular" from_work_dir='samples_stats.tabular' label="${tool.name} on ${on_string}: samples stats">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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273 <filter>matutils_mode['options_mode'] == 'summary' and 'samples' in matutils_mode['summary_options']</filter>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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274 </data>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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275 <data name="clades_stats" format="tabular" from_work_dir='clades_stats.tabular' label="${tool.name} on ${on_string}: clades stats">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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276 <filter>matutils_mode['options_mode'] == 'summary' and 'clades' in matutils_mode['summary_options']</filter>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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277 </data>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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278 <data name="mutations_stats" format="tabular" from_work_dir='mutations_stats.tabular' label="${tool.name} on ${on_string}: mutations stats">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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279 <filter>matutils_mode['options_mode'] == 'summary' and 'mutations' in matutils_mode['summary_options']</filter>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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280 </data>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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281 <data name="aberrant_stats" format="tabular" from_work_dir='aberrant_stats.tabular' label="${tool.name} on ${on_string}: aberrant stats">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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282 <filter>matutils_mode['options_mode'] == 'summary' and 'aberrant' in matutils_mode['summary_options']</filter>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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283 </data>
2
e0a0a473fc1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 5de7b91f2bda9c351f9512601f899248b7278924
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parents: 1
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284 <data name="output_mat" format="protobuf3" from_work_dir='output_mat.pb' label="${tool.name} on ${on_string}: mutation tree">
0
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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285 <filter>matutils_mode['options_mode'] == 'annotate' or matutils_mode['options_mode'] == 'mask'</filter>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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286 </data>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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287 <data name="total_parsimony_tree" format="txt" from_work_dir='output_stdout.txt' label="${tool.name} on ${on_string}: parsimony tree">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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288 <filter>matutils_mode['options_mode'] == 'uncertainty' and 'get-parsimony' in matutils_mode['uncertainty_options']</filter>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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diff changeset
289 </data>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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290 <data name="equally_parsimonious" from_work_dir='equally_parsimonious.tabular' format="tabular" label="${tool.name} on ${on_string}: equally parsimonious placements">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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291 <filter>matutils_mode['options_mode'] == 'uncertainty' and 'find-epps' in matutils_mode['uncertainty_options']</filter>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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diff changeset
292 </data>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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293 <data name="neighbourhood" format="tabular" from_work_dir='neighborhood.tabular' label="${tool.name} on ${on_string}: neighborhood size scores">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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294 <filter>matutils_mode['options_mode'] == 'uncertainty' and 'find-neighborhood' in matutils_mode['uncertainty_options']</filter>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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295 </data>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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296 </outputs>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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297 <tests>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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298 <test expect_num_outputs="3">
1
52fd1d491417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79"
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299 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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300 <conditional name="matutils_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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301 <param name="options_mode" value="extract"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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302 <param name="resolve_polytomies" value="true"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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303 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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304 <conditional name="operation_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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305 <param name="operation" value="samples"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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306 <param name="samples" value="sample_names.txt"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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diff changeset
307 <param name="prune" value="true"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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308 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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309 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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310 <output name="selected_samples" file="test_13_sample_names.txt" ftype="txt"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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311 <output name="path_mutations" file="test_13_path_mutations.tabular" ftype="tabular"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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312 <output name="path_clades" file="test_13_path_clades.tabular" ftype="tabular"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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313 </test>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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314 <test expect_num_outputs="5">
1
52fd1d491417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79"
iuc
parents: 0
diff changeset
315 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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diff changeset
316 <conditional name="matutils_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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317 <param name="options_mode" value="extract"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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318 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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diff changeset
319 <conditional name="operation_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
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diff changeset
320 <param name="operation" value="samples"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
321 <param name="samples" value="sample_names.txt"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
322 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
323 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
324 <output name="selected_samples" file="test_14_sample_names.txt" ftype="txt"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
325 <output name="path_mutations" file="test_14_path_mutations.tabular" ftype="tabular"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
326 <output name="path_clades" file="test_14_path_clades.tabular" ftype="tabular"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
327 <output name="all_paths" file="test_14_all_paths.txt" ftype="txt"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
328 <output name="subtree_vcf" ftype="vcf">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
329 <assert_contents>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
330 <has_size value="7219100" delta="300"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
331 </assert_contents>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
332 </output>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
333 </test>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
334 <test expect_num_outputs="4">
1
52fd1d491417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79"
iuc
parents: 0
diff changeset
335 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
336 <conditional name="matutils_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
337 <param name="options_mode" value="extract"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
338 <param name="outputs_extract" value="write-vcf-no-genotypes,write-mat,write-json,write-tree"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
339 <conditional name="operation_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
340 <param name="operation" value="mutation"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
341 <param name="mutation" value="C241T"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
342 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
343 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
344 <output name="subtree_no_genotype_vcf" file="test_15_subtree_no_genotype.vcf" ftype="vcf"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
345 <output name="mutation_annotated" file="test_15_mutation_annotated_tree.pb" ftype="protobuf3"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
346 <output name="subtree_json" file="test_15_subtree.json" ftype="json"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
347 <output name="tree_newick" file="test_15_tree.nh" ftype="newick"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
348 </test>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
349 <test expect_num_outputs="3">
1
52fd1d491417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79"
iuc
parents: 0
diff changeset
350 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
351 <conditional name="matutils_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
352 <param name="options_mode" value="extract"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
353 <param name="outputs_extract" value="used-samples,sample-paths,write-vcf"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
354 <conditional name="operation_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
355 <param name="operation" value="clades"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
356 <param name="clade" value="B.1.160.7, B.1.258.4"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
357 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
358 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
359 <output name="selected_samples" file="test_16_sample_names.txt" ftype="txt"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
360 <output name="path_mutations" file="test_16_path_mutations.tabular" ftype="tabular"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
361 <output name="subtree_vcf" ftype="vcf">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
362 <assert_contents>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
363 <has_size value="8999600" delta="300"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
364 </assert_contents>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
365 </output>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
366 </test>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
367 <test expect_num_outputs="5">
1
52fd1d491417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79"
iuc
parents: 0
diff changeset
368 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
369 <conditional name="matutils_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
370 <param name="options_mode" value="extract"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
371 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
372 <conditional name="operation_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
373 <param name="operation" value="max-epps"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
374 <param name="max_epps" value="0"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
375 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
376 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
377 <output name="selected_samples" file="test_17_sample_names.txt" ftype="txt"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
378 <output name="path_mutations" file="test_17_path_mutations.tabular" ftype="tabular"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
379 <output name="path_clades" file="test_17_path_clades.tabular" ftype="tabular"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
380 <output name="all_paths" file="test_17_all_paths.txt" ftype="txt"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
381 <output name="subtree_vcf" ftype="vcf">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
382 <assert_contents>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
383 <has_size value="8999600" delta="300"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
384 </assert_contents>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
385 </output>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
386 </test>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
387 <test expect_num_outputs="5">
1
52fd1d491417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79"
iuc
parents: 0
diff changeset
388 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
389 <conditional name="matutils_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
390 <param name="options_mode" value="extract"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
391 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
392 <conditional name="operation_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
393 <param name="operation" value="max-parsimony"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
394 <param name="max_parsimony" value="1"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
395 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
396 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
397 <output name="selected_samples" file="test_18_sample_names.txt" ftype="txt"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
398 <output name="path_mutations" file="test_18_path_mutations.tabular" ftype="tabular"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
399 <output name="path_clades" file="test_18_path_clades.tabular" ftype="tabular"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
400 <output name="all_paths" file="test_18_all_paths.txt" ftype="txt"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
401 <output name="subtree_vcf" ftype="vcf">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
402 <assert_contents>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
403 <has_size value="1183300" delta="300"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
404 </assert_contents>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
405 </output>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
406 </test>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
407 <test expect_num_outputs="3">
1
52fd1d491417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79"
iuc
parents: 0
diff changeset
408 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
409 <conditional name="matutils_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
410 <param name="options_mode" value="extract"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
411 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
412 <conditional name="operation_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
413 <param name="operation" value="max-branch-length"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
414 <param name="max_branch_length" value="2"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
415 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
416 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
417 <output name="selected_samples" file="test_19_sample_names.txt" ftype="txt"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
418 <output name="path_mutations" file="test_19_path_mutations.tabular" ftype="tabular"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
419 <output name="path_clades" file="test_19_path_clades.tabular" ftype="tabular"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
420 </test>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
421 <test expect_num_outputs="1">
1
52fd1d491417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79"
iuc
parents: 0
diff changeset
422 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
423 <conditional name="matutils_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
424 <param name="options_mode" value="summary"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
425 <param name="summary_options" value="general"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
426 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
427 <output name="general_stats" file="test_20_general_stats.txt" ftype="txt"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
428 </test>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
429 <test expect_num_outputs="4">
1
52fd1d491417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79"
iuc
parents: 0
diff changeset
430 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
431 <conditional name="matutils_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
432 <param name="options_mode" value="summary"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
433 <param name="summary_options" value="samples,clades,mutations,aberrant"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
434 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
435 <output name="samples_stats" file="test_21_sample_stats.tabular" ftype="tabular"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
436 <output name="clades_stats" file="test_21_clades_stats.tabular" ftype="tabular"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
437 <output name="mutations_stats" file="test_21_mutations_stats.tabular" ftype="tabular"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
438 <output name="aberrant_stats" file="test_21_aberrant_stats.tabular" ftype="tabular"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
439 </test>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
440 <test expect_num_outputs="1">
1
52fd1d491417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79"
iuc
parents: 0
diff changeset
441 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
442 <conditional name="matutils_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
443 <param name="options_mode" value="uncertainty"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
444 <param name="samples" value="sample_names.txt"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
445 <param name="uncertainty_options" value="get-parsimony"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
446 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
447 <output name="total_parsimony_tree" file="test_22_total_parsimony_tree.txt" ftype="txt"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
448 </test>
79e2ee4e6ebb "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="2">
1
52fd1d491417 "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
79e2ee4e6ebb "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">
79e2ee4e6ebb "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="uncertainty"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
453 <param name="samples" value="sample_names.txt"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
454 <param name="uncertainty_options" value="find-epps,find-neighborhood"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
455 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
456 <output name="equally_parsimonious" file="test_23_equally_parsimoniou.tabular" ftype="tabular"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
457 <output name="neighbourhood" file="test_23_neighbourhood.tabular" ftype="tabular"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
458 </test>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
459 <test expect_num_outputs="1">
1
52fd1d491417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79"
iuc
parents: 0
diff changeset
460 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
461 <conditional name="matutils_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
462 <param name="options_mode" value="mask"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
463 <param name="restricted_samples" value="sample_names.txt"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
464 <param name="simplify" value="true"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
465 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
466 <output name="output_mat" file="test_24_restricted.pb" ftype="protobuf3"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
467 </test>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
468 <test expect_num_outputs="1">
1
52fd1d491417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79"
iuc
parents: 0
diff changeset
469 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
0
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
470 <conditional name="matutils_mode">
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
471 <param name="options_mode" value="mask"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
472 <param name="rename_samples" value="rename_samples.tabular"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
473 </conditional>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
474 <output name="output_mat" file="test_25_renamed.pb" ftype="protobuf3"/>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
475 </test>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
476 </tests>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
477 <help><![CDATA[
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
478
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
479 .. class:: infomark
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
480
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
481 **Purpose**
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
482
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
483 matUtils is a suite of tools used to analyze, edit, and manipulate mutation annotated tree (.pb) files.
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
484
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
485 ----
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
486
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
487 .. class:: infomark
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
488
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
489 **matUtils Common Options**
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
iuc
parents:
diff changeset
490
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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491 **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.
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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492 **Sumary**: matUtils summary is used to get basic statistics and attribute information about the mat.
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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493 **Annotate**: matUtils annotate is a function for adding clade annotation information to the pb.
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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494 **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.
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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495 **Mask**: matUtils mask is used to mask specific samples out of the pb, removing their mutations from visibility.
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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496
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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497 You can find more information in the `matUtils official documentation page <https://usher-wiki.readthedocs.io/en/latest/matUtils.html>`_.
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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498
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499 ]]> </help>
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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500 <expand macro="citations" />
79e2ee4e6ebb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
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501 </tool>