comparison matutils.xml @ 1:52fd1d491417 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79"

0:79e2ee4e6ebb

            <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"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="extract"/>
                <param name="resolve_polytomies" value="true"/>
                <param name="outputs_extract" value="used-samples,sample-paths,clade-paths"/>
                <conditional name="operation_mode">

            <output name="selected_samples" file="test_13_sample_names.txt" ftype="txt"/>
            <output name="path_mutations" file="test_13_path_mutations.tabular" ftype="tabular"/>
            <output name="path_clades" file="test_13_path_clades.tabular" ftype="tabular"/>
        </test>
        <test expect_num_outputs="5">
            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="extract"/>
                <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/>
                <conditional name="operation_mode">
                    <param name="operation" value="samples"/>

                    <has_size value="7219100" delta="300"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="4">
            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="extract"/>
                <param name="outputs_extract" value="write-vcf-no-genotypes,write-mat,write-json,write-tree"/>
                <conditional name="operation_mode">
                    <param name="operation" value="mutation"/>

            <output name="mutation_annotated" file="test_15_mutation_annotated_tree.pb" ftype="protobuf3"/>
            <output name="subtree_json" file="test_15_subtree.json" ftype="json"/>
            <output name="tree_newick" file="test_15_tree.nh" ftype="newick"/>
        </test>
        <test expect_num_outputs="3">
            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
            <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"/>

                    <has_size value="8999600" delta="300"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="5">
            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="extract"/>
                <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/>
                <conditional name="operation_mode">
                    <param name="operation" value="max-epps"/>

                    <has_size value="8999600" delta="300"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="5">
            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="extract"/>
                <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/>
                <conditional name="operation_mode">
                    <param name="operation" value="max-parsimony"/>

                    <has_size value="1183300" delta="300"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="extract"/>
                <param name="outputs_extract" value="used-samples,sample-paths,clade-paths"/>
                <conditional name="operation_mode">
                    <param name="operation" value="max-branch-length"/>

            <output name="selected_samples" file="test_19_sample_names.txt" ftype="txt"/>
            <output name="path_mutations" file="test_19_path_mutations.tabular" ftype="tabular"/>
            <output name="path_clades" file="test_19_path_clades.tabular" ftype="tabular"/>
        </test>
        <test expect_num_outputs="1">
            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
            <conditional name="matutils_mode">
                <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"/>
            <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"/>
            <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"/>
            <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"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="mask"/>
                <param name="restricted_samples" value="sample_names.txt"/>
                <param name="simplify" value="true"/>
            </conditional>
            <output name="output_mat" file="test_24_restricted.pb" ftype="protobuf3"/>
        </test>
        <test expect_num_outputs="1">
            <param name="mutation_annotation_file" value="mutation_annotation.pb"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="mask"/>
                <param name="rename_samples" value="rename_samples.tabular"/>
            </conditional>
            <output name="output_mat" file="test_25_renamed.pb" ftype="protobuf3"/>

1:52fd1d491417

            <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 name="matutils_mode">
                <param name="options_mode" value="extract"/>
                <param name="resolve_polytomies" value="true"/>
                <param name="outputs_extract" value="used-samples,sample-paths,clade-paths"/>
                <conditional name="operation_mode">

            <output name="selected_samples" file="test_13_sample_names.txt" ftype="txt"/>
            <output name="path_mutations" file="test_13_path_mutations.tabular" ftype="tabular"/>
            <output name="path_clades" file="test_13_path_clades.tabular" ftype="tabular"/>
        </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"/>
                <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/>
                <conditional name="operation_mode">
                    <param name="operation" value="samples"/>

                    <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"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="extract"/>
                <param name="outputs_extract" value="write-vcf-no-genotypes,write-mat,write-json,write-tree"/>
                <conditional name="operation_mode">
                    <param name="operation" value="mutation"/>

            <output name="mutation_annotated" file="test_15_mutation_annotated_tree.pb" ftype="protobuf3"/>
            <output name="subtree_json" file="test_15_subtree.json" ftype="json"/>
            <output name="tree_newick" file="test_15_tree.nh" ftype="newick"/>
        </test>
        <test expect_num_outputs="3">
            <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"/>

                    <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"/>
                <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/>
                <conditional name="operation_mode">
                    <param name="operation" value="max-epps"/>

                    <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"/>
                <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/>
                <conditional name="operation_mode">
                    <param name="operation" value="max-parsimony"/>

                    <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"/>
            <conditional name="matutils_mode">
                <param name="options_mode" value="extract"/>
                <param name="outputs_extract" value="used-samples,sample-paths,clade-paths"/>
                <conditional name="operation_mode">
                    <param name="operation" value="max-branch-length"/>

            <output name="selected_samples" file="test_19_sample_names.txt" ftype="txt"/>
            <output name="path_mutations" file="test_19_path_mutations.tabular" ftype="tabular"/>
            <output name="path_clades" file="test_19_path_clades.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="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"/>
                <param name="restricted_samples" value="sample_names.txt"/>
                <param name="simplify" value="true"/>
            </conditional>
            <output name="output_mat" file="test_24_restricted.pb" ftype="protobuf3"/>
        </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"/>
                <param name="rename_samples" value="rename_samples.tabular"/>
            </conditional>
            <output name="output_mat" file="test_25_renamed.pb" ftype="protobuf3"/>