comparison matutils.xml @ 2:daa704d3ac8f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher commit d44fdcd836306a2096d50bebb28d8faacdb0fbfd

1:75e51e947a98

<tool id='usher_matutils' name='UShER matUtils' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.01'>
    <description>analyze, edit, and manipulate mutation annotated tree files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro='edam_ontology' />
    <expand macro='requirements' />
    <version_command>usher --version</version_command>
    <command detect_errors='exit_code'><![CDATA[
        matUtils
        $matutils_mode.options_mode
        --input-mat $mutation_annotation_file
        #if $matutils_mode.options_mode == 'extract'
            #if $matutils_mode.operation_mode.operation == 'samples'
                #if $matutils_mode.operation_mode.samples
                    --samples '${matutils_mode.operation_mode.samples}'
                #end if
                $matutils_mode.operation_mode.prune
            #elif $matutils_mode.operation_mode.operation == 'clade'
                --clade '${matutils_mode.operation_mode.clade}'
                $matutils_mode.operation_mode.prune
            #elif $matutils_mode.operation_mode.operation == 'mutation'
                --mutation '${matutils_mode.operation_mode.mutation}'
                $matutils_mode.operation_mode.prune
            #elif $matutils_mode.operation_mode.operation == 'max-epps'
                --max-epps $matutils_mode.operation_mode.max_epps
                $matutils_mode.operation_mode.prune
            #elif $matutils_mode.operation_mode.operation == 'max-parsimony'
                --max-parsimony $matutils_mode.operation_mode.max_parsimony
                $matutils_mode.operation_mode.prune
            #elif $matutils_mode.operation_mode.operation == 'nearest-k'
                --nearest-k '${matutils_mode.operation_mode.nearest_k}'
                $matutils_mode.operation_mode.prune
            #elif $matutils_mode.operation_mode.operation == 'max-branch-length'
                --max-branch-length $matutils_mode.operation_mode.max_branch_length
            #end if
            $matutils_mode.get_representative
            $matutils_mode.resolve_polytomies
            #if 'used-samples' in $matutils_mode.outputs_extract
                --used-samples selected_samples.txt ##$selected_samples
            #end if
            #if 'sample-paths' in $matutils_mode.outputs_extract
                --sample-paths path_mutations.tabular ##$path_mutations
            #end if
            #if 'clade-paths' in $matutils_mode.outputs_extract
                --clade-paths path_clades.tabular ##$path_clades
            #end if
            #if 'all-paths' in $matutils_mode.outputs_extract
                --all-paths all_paths.txt ##$all_paths
            #end if
            #if 'write-vcf' in $matutils_mode.outputs_extract
                --write-vcf subtree_vcf.vcf ##$subtree_vcf
            #end if
            #if 'write-vcf-no-genotypes' in $matutils_mode.outputs_extract and 'write-vcf' not in $matutils_mode.outputs_extract
                --write-vcf subtree_vcf_no_genotypes.vcf --no-genotypes
            #end if
            #if 'write-mat' in $matutils_mode.outputs_extract
                --write-mat mutation_annotated.pb ##$mutation_annotated
            #end if
            #if 'write-mat-collapsed' in $matutils_mode.outputs_extract and 'write-mat' not in $matutils_mode.outputs_extract
                --write-mat mutation_annotated_collapsed.pb --collapsed-tree
            #end if
            #if 'write-json' in $matutils_mode.outputs_extract
                --write-json subtree_json.json ##$subtree_json
            #end if
            #if 'write-tree' in $matutils_mode.outputs_extract
                --write-tree tree_newick.nh ##$tree_newick
            #end if
            #if 'write-tree-retain-branch' in $matutils_mode.outputs_extract and 'write-tree' not in $matutils_mode.outputs_extract
                --write-tree tree_newick_retain_branch.nh --retain-branch-length
            #end if
        #elif $matutils_mode.options_mode == 'summary'
            #if 'samples' in $matutils_mode.summary_options
                --samples samples_stats.tabular
            #end if
            #if 'clades' in $matutils_mode.summary_options
                --clades clades_stats.tabular
            #end if
            #if 'mutations' in $matutils_mode.summary_options
                --mutations mutations_stats.tabular
            #end if
            #if 'aberrant' in $matutils_mode.summary_options
                --aberrant aberrant_stats.tabular
            #end if
            --output-directory ./
        #elif $matutils_mode.options_mode == 'annotate'
            #if $matutils_mode.clade_names
                --clade-names '${matutils_mode.clade_names}'
                #if $matutils_mode.allele_frequency
                    --allele-frequency $matutils_mode.allele_frequency
                #end if
                #if $matutils_mode.set_overlap
                    --set-overlap $matutils_mode.set_overlap
                #end if
                #if $matutils_mode.mask_frequency
                    --mask-frequency $matutils_mode.mask_frequency
                #end if
                #if $matutils_mode.clip_sample_frequency
                    --clip-sample-frequency $matutils_mode.clip_sample_frequency
                #end if
            #end if
            #if $matutils_mode.clade_to_nid
                --clade-to-nid '${matutils_mode.clade_to_nid}'
            #end if
            $matutils_mode.clear_current
            --output-mat output_mat.pb ##$output_mat
        #elif $matutils_mode.options_mode == 'uncertainty'
            --samples '${matutils_mode.samples}'
            #if 'get-parsimony' in $matutils_mode.uncertainty_options
                --get-parsimony
            #end if
            #if 'find-epps' in $matutils_mode.uncertainty_options
                --find-epps equally_parsimonious.tabular
            #end if
            #if 'find-neighborhood' in $matutils_mode.uncertainty_options
                --find-neighborhood neighborhood.tabular
            #end if
        #elif $matutils_mode.options_mode == 'mask'
            #if $matutils_mode.restricted_samples
                --restricted-samples '${matutils_mode.restricted_samples}'
            #end if
            #if $matutils_mode.rename_samples
                --rename-samples '${matutils_mode.rename_samples}'
            #end if
            $$matutils_mode.simplify
            --output-mat output_mat.pb ##$output_mat
        #end if
        --threads \${GALAXY_SLOTS:-1} > output_stdout.txt

    ]]>    </command>
    <inputs>
        <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)."/>
        <conditional name="matutils_mode">
            <param name="options_mode" type="select" label="matUtils mode">
                <option value="extract">Extract: subsetting and converting a MAT pb to other file formats</option>

            <when value="summary">
                <param name="summary_options" type="select" display="checkboxes" multiple="true" label="Select statistics and attribute information">
                    <option value="general">Number of nodes, number of samples, number of condensed nodes, and total tree parsimony</option>
                    <option value="samples">Samples in the tree and their parsimony score (--samples)</option>
                    <option value="clades">Clades and the count of associated samples in the tree (--clades)</option>
                    <option value="mutations">Mutations in the tree and their occurrence count (--mutations)</option>
                    <option value="aberrant">Potentially problematic nodes (--aberrant)</option>
                </param>
            </when>
            <when value="annotate">
                <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."/>
                <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."/>                

                <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." />
            </when>
            <when value="uncertainty">
                <param argument="--samples" type="data" format="txt" label="Select samples by explicitly naming them, one per line in a plain text file" />
                <param name="uncertainty_options" type="select" display="checkboxes" multiple="true" label="Metrics for sample placement certainty">
                    <option value="get-parsimony">Total tree parsimony score (--get-parsimony)</option>
                    <option value="find-epps">Number of equally parsimonious placements for each sample (--find-epps)</option>
                    <option value="find-neighborhood">Neighborhood size scores (--find-neighborhood)</option>
                </param>
            </when>
            <when value="mask">
                <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"/>
                <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"/>
                <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" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="selected_samples" format="txt" from_work_dir='selected_samples.txt' label="${tool.name} on ${on_string}: selected samples">

            <filter>matutils_mode['options_mode'] == 'summary' and 'samples' in matutils_mode['summary_options']</filter>
        </data>  
        <data name="clades_stats" format="tabular" from_work_dir='clades_stats.tabular' label="${tool.name} on ${on_string}: clades stats">
            <filter>matutils_mode['options_mode'] == 'summary' and 'clades' in matutils_mode['summary_options']</filter>
        </data>  
        <data name="mutations_stats" format="tabular" from_work_dir='mutations_stats.tabular' label="${tool.name} on ${on_string}: mutations stats">
            <filter>matutils_mode['options_mode'] == 'summary' and 'mutations' in matutils_mode['summary_options']</filter>
        </data>  
        <data name="aberrant_stats" format="tabular" from_work_dir='aberrant_stats.tabular' label="${tool.name} on ${on_string}: aberrant stats">
            <filter>matutils_mode['options_mode'] == 'summary' and 'aberrant' in matutils_mode['summary_options']</filter>
        </data>  
        <data name="output_mat" format="protobuf3" from_work_dir='output_mat.pb' label="${tool.name} on ${on_string}: mutation annotated tree">
            <filter>matutils_mode['options_mode'] == 'annotate' or matutils_mode['options_mode'] == 'mask'</filter>
        </data>  
        <data name="total_parsimony_tree" format="txt" from_work_dir='output_stdout.txt' label="${tool.name} on ${on_string}: parsimony tree">
            <filter>matutils_mode['options_mode'] == 'uncertainty' and 'get-parsimony' in matutils_mode['uncertainty_options']</filter>
        </data>  
        <data name="equally_parsimonious" from_work_dir='equally_parsimonious.tabular' format="tabular" label="${tool.name} on ${on_string}: equally parsimonious placements">
            <filter>matutils_mode['options_mode'] == 'uncertainty' and 'find-epps' in matutils_mode['uncertainty_options']</filter>
        </data>  
        <data name="neighbourhood" format="tabular" from_work_dir='neighborhood.tabular' label="${tool.name} on ${on_string}: neighborhood size scores">
            <filter>matutils_mode['options_mode'] == 'uncertainty' and 'find-neighborhood' in matutils_mode['uncertainty_options']</filter>
        </data>  
    </outputs>
    <tests>
        <test expect_num_outputs="3">
            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>

            </conditional>
            <output name="selected_samples" file="test_14_sample_names.txt" ftype="txt"/>
            <output name="path_mutations" file="test_14_path_mutations.tabular" ftype="tabular"/>
            <output name="path_clades" file="test_14_path_clades.tabular" ftype="tabular"/>
            <output name="all_paths" file="test_14_all_paths.txt" ftype="txt"/>
            <output name="subtree_vcf" ftype="vcf">
                <assert_contents>
                    <has_size value="7219100" delta="300"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="4">
            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>

            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="extract"/>
                <param name="outputs_extract" value="used-samples,sample-paths,write-vcf"/>
                <conditional name="operation_mode">
                    <param name="operation" value="clades"/>
                    <param name="clade" value="B.1.160.7, B.1.258.4"/>
                </conditional>
            </conditional>
            <output name="selected_samples" file="test_16_sample_names.txt" ftype="txt"/>
            <output name="path_mutations" file="test_16_path_mutations.tabular" ftype="tabular"/>
            <output name="subtree_vcf" ftype="vcf">
                <assert_contents>
                    <has_size value="8999600" delta="300"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="5">
            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="extract"/>

            </conditional>
            <output name="selected_samples" file="test_17_sample_names.txt" ftype="txt"/>
            <output name="path_mutations" file="test_17_path_mutations.tabular" ftype="tabular"/>
            <output name="path_clades" file="test_17_path_clades.tabular" ftype="tabular"/>
            <output name="all_paths" file="test_17_all_paths.txt" ftype="txt"/>
            <output name="subtree_vcf" ftype="vcf">
                <assert_contents>
                    <has_size value="8999600" delta="300"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="5">
            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>

            </conditional>
            <output name="selected_samples" file="test_18_sample_names.txt" ftype="txt"/>
            <output name="path_mutations" file="test_18_path_mutations.tabular" ftype="tabular"/>
            <output name="path_clades" file="test_18_path_clades.tabular" ftype="tabular"/>
            <output name="all_paths" file="test_18_all_paths.txt" ftype="txt"/>
            <output name="subtree_vcf" ftype="vcf">
                <assert_contents>
                    <has_size value="1183300" delta="300"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>

                <param name="options_mode" value="summary"/>
                <param name="summary_options" value="general"/>
            </conditional>
            <output name="general_stats" file="test_20_general_stats.txt" ftype="txt"/>
        </test>
        <test expect_num_outputs="4">
            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="summary"/>
                <param name="summary_options" value="samples,clades,mutations,aberrant"/>
            </conditional>
            <output name="samples_stats" file="test_21_sample_stats.tabular" ftype="tabular"/>
            <output name="clades_stats" file="test_21_clades_stats.tabular" ftype="tabular"/>
            <output name="mutations_stats" file="test_21_mutations_stats.tabular" ftype="tabular"/>
            <output name="aberrant_stats" file="test_21_aberrant_stats.tabular" ftype="tabular"/>       
        </test>
        <test expect_num_outputs="1">
            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="uncertainty"/>
                <param name="samples" value="sample_names.txt"/>
                <param name="uncertainty_options" value="get-parsimony"/>
            </conditional>
            <output name="total_parsimony_tree" file="test_22_total_parsimony_tree.txt" ftype="txt"/>
        </test>
        <test expect_num_outputs="2">
            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="uncertainty"/>
                <param name="samples" value="sample_names.txt"/>
                <param name="uncertainty_options" value="find-epps,find-neighborhood"/>
            </conditional>
            <output name="equally_parsimonious" file="test_23_equally_parsimoniou.tabular" ftype="tabular"/>
            <output name="neighbourhood" file="test_23_neighbourhood.tabular" ftype="tabular"/>
        </test>
        <test expect_num_outputs="1">
            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="mask"/>

2:daa704d3ac8f

<tool id='usher_matutils' name='UShER matUtils' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' profile='@PROFILE@'>
    <description>analyze, edit, and manipulate mutation annotated tree files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro='requirements' />
    <expand macro="version"/>
    <command detect_errors='exit_code'><![CDATA[
    ## get correct extension filenames
    ln -sf '$mutation_annotation_file' '$mutation_annotation_file.element_identifier' &&
    
    matUtils
    $matutils_mode.options_mode
    --input-mat '$mutation_annotation_file.element_identifier'

    #if $matutils_mode.options_mode == 'extract'
        #if $matutils_mode.operation_mode.operation == 'samples'
            #if $matutils_mode.operation_mode.samples
                --samples '${matutils_mode.operation_mode.samples}'
            #end if
            $matutils_mode.operation_mode.prune
        #elif $matutils_mode.operation_mode.operation == 'clade'
            --clade '${matutils_mode.operation_mode.clade}'
            $matutils_mode.operation_mode.prune
        #elif $matutils_mode.operation_mode.operation == 'mutation'
            --mutation '${matutils_mode.operation_mode.mutation}'
            $matutils_mode.operation_mode.prune
        #elif $matutils_mode.operation_mode.operation == 'max-epps'
            --max-epps $matutils_mode.operation_mode.max_epps
            $matutils_mode.operation_mode.prune
        #elif $matutils_mode.operation_mode.operation == 'max-parsimony'
            --max-parsimony $matutils_mode.operation_mode.max_parsimony
            $matutils_mode.operation_mode.prune
        #elif $matutils_mode.operation_mode.operation == 'nearest-k'
            --nearest-k '${matutils_mode.operation_mode.nearest_k}'
            $matutils_mode.operation_mode.prune
        #elif $matutils_mode.operation_mode.operation == 'max-branch-length'
            --max-branch-length $matutils_mode.operation_mode.max_branch_length
        #end if
        $matutils_mode.get_representative
        $matutils_mode.resolve_polytomies
        #if 'used-samples' in $matutils_mode.outputs_extract
            --used-samples selected_samples.txt ##$selected_samples
        #end if
        #if 'sample-paths' in $matutils_mode.outputs_extract
            --sample-paths path_mutations.tabular ##$path_mutations
        #end if
        #if 'clade-paths' in $matutils_mode.outputs_extract
            --clade-paths path_clades.tabular ##$path_clades
        #end if
        #if 'all-paths' in $matutils_mode.outputs_extract
            --all-paths all_paths.txt ##$all_paths
        #end if
        #if 'write-vcf' in $matutils_mode.outputs_extract
            --write-vcf subtree_vcf.vcf ##$subtree_vcf
        #end if
        #if 'write-vcf-no-genotypes' in $matutils_mode.outputs_extract and 'write-vcf' not in $matutils_mode.outputs_extract
            --write-vcf subtree_vcf_no_genotypes.vcf --no-genotypes
        #end if
        #if 'write-mat' in $matutils_mode.outputs_extract
            --write-mat mutation_annotated.pb ##$mutation_annotated
        #end if
        #if 'write-mat-collapsed' in $matutils_mode.outputs_extract and 'write-mat' not in $matutils_mode.outputs_extract
            --write-mat mutation_annotated_collapsed.pb --collapsed-tree
        #end if
        #if 'write-json' in $matutils_mode.outputs_extract
            --write-json subtree_json.json ##$subtree_json
        #end if
        #if 'write-tree' in $matutils_mode.outputs_extract
            --write-tree tree_newick.nh ##$tree_newick
        #end if
        #if 'write-tree-retain-branch' in $matutils_mode.outputs_extract and 'write-tree' not in $matutils_mode.outputs_extract
            --write-tree tree_newick_retain_branch.nh --retain-branch-length
        #end if

    #elif $matutils_mode.options_mode == 'summary'
        #if 'samples' in $matutils_mode.summary_options
            --samples samples_stats.tabular
        #end if
        #if 'clades' in $matutils_mode.summary_options
            --clades clades_stats.tabular
        #end if
        #if 'sample_clades' in $matutils_mode.summary_options
            --sample-clades sampleclades_stats.tabular
        #end if
        #if 'mutations' in $matutils_mode.summary_options
            --mutations mutations_stats.tabular
        #end if
        #if 'aberrant' in $matutils_mode.summary_options
            --aberrant aberrant_stats.tabular
        #end if
        #if 'haplotype' in $matutils_mode.summary_options
            --haplotype haplotype_stats.tabular
        #end if
        #if 'calculate_roho' in $matutils_mode.summary_options
            --calculate-roho roho_stats.tabular
        #end if
        #if 'node_stats' in $matutils_mode.summary_options
            --node-stats node_stats.tabular
        #end if
        --output-directory ./

    #elif $matutils_mode.options_mode == 'annotate'
        #if $matutils_mode.clade_names
            --clade-names '${matutils_mode.clade_names}'
            #if $matutils_mode.allele_frequency
                --allele-frequency $matutils_mode.allele_frequency
            #end if
            #if $matutils_mode.set_overlap
                --set-overlap $matutils_mode.set_overlap
            #end if
            #if $matutils_mode.mask_frequency
                --mask-frequency $matutils_mode.mask_frequency
            #end if
            #if $matutils_mode.clip_sample_frequency
                --clip-sample-frequency $matutils_mode.clip_sample_frequency
            #end if
        #end if
        #if $matutils_mode.clade_to_nid
            --clade-to-nid '${matutils_mode.clade_to_nid}'
        #end if
        $matutils_mode.clear_current
        --output-mat output_mat.pb ##$output_mat

    #elif $matutils_mode.options_mode == 'uncertainty'
        --samples '${matutils_mode.samples}'
        #if 'find-epps' in $matutils_mode.uncertainty_options
            --find-epps equally_parsimonious.tabular
        #end if
        #if 'record-placements' in $matutils_mode.uncertainty_options
            --record-placements parent_placements.tabular
        #end if

    #elif $matutils_mode.options_mode == 'mask'
        #if $matutils_mode.restricted_samples
            --restricted-samples '${matutils_mode.restricted_samples}'
        #end if
        #if $matutils_mode.rename_samples
            --rename-samples '${matutils_mode.rename_samples}'
        #end if
        #if $matutils_mode.mask_mutations
            --mask-mutations '${matutils_mode.mask_mutations}'
        #end if
        $matutils_mode.simplify
        $matutils_mode.condense_tree
        --output-mat output_mat.pb ##$output_mat
    #end if

    --threads \${GALAXY_SLOTS:-1} > output_stdout.txt

]]> </command>
    <inputs>
        <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)."/>
        <conditional name="matutils_mode">
            <param name="options_mode" type="select" label="matUtils mode">
                <option value="extract">Extract: subsetting and converting a MAT pb to other file formats</option>

            <when value="summary">
                <param name="summary_options" type="select" display="checkboxes" multiple="true" label="Select statistics and attribute information">
                    <option value="general">Number of nodes, number of samples, number of condensed nodes, and total tree parsimony</option>
                    <option value="samples">Samples in the tree and their parsimony score (--samples)</option>
                    <option value="clades">Clades and the count of associated samples in the tree (--clades)</option>
                    <option value="sample_clades">All samples and their associated clade values (--sample-clades)</option>
                    <option value="mutations">Mutations in the tree and their occurrence count (--mutations)</option>
                    <option value="aberrant">Potentially problematic nodes (--aberrant)</option>
                    <option value="haplotype">Haplotypes and their total frequency (--haplotype)</option>
                    <option value="calculate_roho">Distribution of RoHO values for all homoplasic mutations (--calculate-roho)</option>
                    <option value="node_stats">Per internal node, the number of descendents, mutations, mutational density, and reversion mutations (--node-stats)</option>
                </param>
            </when>
            <when value="annotate">
                <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."/>
                <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."/>                

                <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." />
            </when>
            <when value="uncertainty">
                <param argument="--samples" type="data" format="txt" label="Select samples by explicitly naming them, one per line in a plain text file" />
                <param name="uncertainty_options" type="select" display="checkboxes" multiple="true" label="Metrics for sample placement certainty">
                    <option value="find-epps">Number of equally parsimonious placements for each sample (--find-epps)</option>
                    <option value="record-placements">Record potential parents for each sample (--record-placements)</option>
                </param>
            </when>
            <when value="mask">
                <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"/>
                <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"/>
                <param argument="--mask-mutations" type="data" format="tabular" optional="True" label="TSV or CSV containing mutations to be masked in the first column and locations to mask downstream from in the second."/>
                <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" />
                <param argument="--condense-tree" type="boolean" truevalue="--condense-tree" falsevalue="" label="Use to recondense the tree before saving." />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="selected_samples" format="txt" from_work_dir='selected_samples.txt' label="${tool.name} on ${on_string}: selected samples">

            <filter>matutils_mode['options_mode'] == 'summary' and 'samples' in matutils_mode['summary_options']</filter>
        </data>  
        <data name="clades_stats" format="tabular" from_work_dir='clades_stats.tabular' label="${tool.name} on ${on_string}: clades stats">
            <filter>matutils_mode['options_mode'] == 'summary' and 'clades' in matutils_mode['summary_options']</filter>
        </data>  
        <data name="sampleclades_stats" format="tabular" from_work_dir='sampleclades_stats.tabular' label="${tool.name} on ${on_string}: sample - clades stats">
            <filter>matutils_mode['options_mode'] == 'summary' and 'sample_clades' in matutils_mode['summary_options']</filter>
        </data>  

        <data name="mutations_stats" format="tabular" from_work_dir='mutations_stats.tabular' label="${tool.name} on ${on_string}: mutations stats">
            <filter>matutils_mode['options_mode'] == 'summary' and 'mutations' in matutils_mode['summary_options']</filter>
        </data>  
        <data name="aberrant_stats" format="tabular" from_work_dir='aberrant_stats.tabular' label="${tool.name} on ${on_string}: aberrant stats">
            <filter>matutils_mode['options_mode'] == 'summary' and 'aberrant' in matutils_mode['summary_options']</filter>
        </data>  
        <data name="haplotype_stats" format="tabular" from_work_dir='haplotype_stats.tabular' label="${tool.name} on ${on_string}: haplotype stats">
            <filter>matutils_mode['options_mode'] == 'summary' and 'haplotype' in matutils_mode['summary_options']</filter>
        </data>  
        <data name="roho_stats" format="tabular" from_work_dir='roho_stats.tabular' label="${tool.name} on ${on_string}: RoHo stats">
            <filter>matutils_mode['options_mode'] == 'summary' and 'calculate_roho' in matutils_mode['summary_options']</filter>
        </data>  
        <data name="node_stats" format="tabular" from_work_dir='node_stats.tabular' label="${tool.name} on ${on_string}: node stats">
            <filter>matutils_mode['options_mode'] == 'summary' and 'node_stats' in matutils_mode['summary_options']</filter>
        </data>  
        <data name="output_mat" format="protobuf3" from_work_dir='output_mat.pb' label="${tool.name} on ${on_string}: mutation tree">
            <filter>matutils_mode['options_mode'] == 'annotate' or matutils_mode['options_mode'] == 'mask'</filter>
        </data>  
        <data name="equally_parsimonious" from_work_dir='equally_parsimonious.tabular' format="tabular" label="${tool.name} on ${on_string}: equally parsimonious placements">
            <filter>matutils_mode['options_mode'] == 'uncertainty' and 'find-epps' in matutils_mode['uncertainty_options']</filter>
        </data>  
        <data name="parent_placements" format="tabular" from_work_dir='parent_placements.tabular' label="${tool.name} on ${on_string}: Potential parents">
            <filter>matutils_mode['options_mode'] == 'uncertainty' and 'record-placements' in matutils_mode['uncertainty_options']</filter>
        </data>  
    </outputs>
    <tests>
        <test expect_num_outputs="3">
            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>

            </conditional>
            <output name="selected_samples" file="test_14_sample_names.txt" ftype="txt"/>
            <output name="path_mutations" file="test_14_path_mutations.tabular" ftype="tabular"/>
            <output name="path_clades" file="test_14_path_clades.tabular" ftype="tabular"/>
            <output name="all_paths" file="test_14_all_paths.txt" ftype="txt"/>
            <output name="subtree_vcf" ftype="vcf" >
                <assert_contents>
                    <has_line line="##fileformat=VCFv4.2" />
                    <has_line_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT.+" />
                    <has_n_columns n="1105" comment="#" />
                    <has_n_lines n="3204" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="4">
            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>

            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="extract"/>
                <param name="outputs_extract" value="used-samples,sample-paths,write-vcf"/>
                <conditional name="operation_mode">
                    <param name="operation" value="clade"/>
                    <param name="clade" value="B.1.160.7,B.1.258.4"/>
                </conditional>
            </conditional>
            <output name="selected_samples" file="test_16_sample_names.txt" ftype="txt"/>
            <output name="path_mutations" file="test_16_path_mutations.tabular" ftype="tabular"/>
            <output name="subtree_vcf" file="test_16_subtree.vcf" ftype="vcf" />
        </test>
        <test expect_num_outputs="5">
            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="extract"/>

            </conditional>
            <output name="selected_samples" file="test_17_sample_names.txt" ftype="txt"/>
            <output name="path_mutations" file="test_17_path_mutations.tabular" ftype="tabular"/>
            <output name="path_clades" file="test_17_path_clades.tabular" ftype="tabular"/>
            <output name="all_paths" file="test_17_all_paths.txt" ftype="txt"/>
            <output name="subtree_vcf" ftype="vcf" >
                <assert_contents>
                    <has_line line="##fileformat=VCFv4.2" />
                    <has_line_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT.+" />
                    <has_n_columns n="1243" comment="#" />
                    <has_n_lines n="3558" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="5">
            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>

            </conditional>
            <output name="selected_samples" file="test_18_sample_names.txt" ftype="txt"/>
            <output name="path_mutations" file="test_18_path_mutations.tabular" ftype="tabular"/>
            <output name="path_clades" file="test_18_path_clades.tabular" ftype="tabular"/>
            <output name="all_paths" file="test_18_all_paths.txt" ftype="txt"/>
            <output name="subtree_vcf" ftype="vcf" >
                <assert_contents>
                    <has_line line="##fileformat=VCFv4.2" />
                    <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT.+" />
                    <has_n_columns n="450" comment="#" />
                    <has_n_lines n="1256" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>

                <param name="options_mode" value="summary"/>
                <param name="summary_options" value="general"/>
            </conditional>
            <output name="general_stats" file="test_20_general_stats.txt" ftype="txt"/>
        </test>
        <test expect_num_outputs="8">
            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="summary"/>
                <param name="summary_options" value="samples,clades,mutations,aberrant,sample_clades,haplotype,calculate_roho,node_stats"/>
            </conditional>
            <output name="samples_stats" file="test_21_sample_stats.tabular" ftype="tabular"/>
            <output name="clades_stats" file="test_21_clades_stats.tabular" ftype="tabular"/>
            <output name="mutations_stats" file="test_21_mutations_stats.tabular" ftype="tabular"/>
            <output name="aberrant_stats" file="test_21_aberrant_stats.tabular" ftype="tabular"/>       
            <output name="sampleclades_stats" file="test_21_sampleclades_stats.tabular" ftype="tabular"/>       
            <output name="haplotype_stats" file="test_21_haplotype_stats.tabular" ftype="tabular"/>       
            <output name="roho_stats" file="test_21_roho_stats.tabular" ftype="tabular"/>       
            <output name="node_stats" file="test_21_node_stats.tabular" ftype="tabular"/>       
        </test>
        <test expect_num_outputs="1">
            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="uncertainty"/>
                <param name="samples" value="sample_names.txt"/>
                <param name="uncertainty_options" value="record-placements"/>
            </conditional>
            <output name="parent_placements" ftype="tabular" >
                <assert_contents>
                    <has_line_matching expression="placement\tsample" />
                    <has_n_columns n="2" />
                    <has_n_lines n="3240" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="uncertainty"/>
                <param name="samples" value="sample_names.txt"/>
                <param name="uncertainty_options" value="find-epps"/>
            </conditional>
            <output name="equally_parsimonious" file="test_23_equally_parsimonious.tabular" ftype="tabular"/>
        </test>
        <test expect_num_outputs="1">
            <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="mask"/>