comparison usher.xml @ 3:746b434c8fbb draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 5de7b91f2bda9c351f9512601f899248b7278924

2:8f6c7638eab2

<tool id='usher' name='UShER' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.01'>
    <description>ultrafast sample placement on existing trees</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[
        #if $vcf.ext == 'vcf_bgzip':
            ln -s '$vcf' input.vcf.gz &&

        #end if
        $output_options.write_parsimony_scores_per_node
        #if $output_options.multiple_placements
            -M $output_options.multiple_placements
        #end if
        #if $retain_input_branch_lengths
            $retain_input_branch_lengths
        #end if
        -T \${GALAXY_SLOTS:-1}
        -d ./
        #if $output_options.write_subtrees_size
            && mkdir -p out_subtrees out_subtrees_expanded out_subtrees_mutations
            && mv subtree*expanded.txt ./out_subtrees_expanded

            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="vcf" value="new_samples.vcf.gz" ftype="vcf_bgzip"/>
            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
            <param name="retain_input_branch" value="true"/>
            <output name="final_tree" file="test_12_final_tree.nh" ftype="newick" lines_diff="2"/>
            <output name="mutation_paths" file="test_12_mutation_path.nh" ftype="txt"/>
            <output name="clades" ftype="txt">
                <assert_contents>
                    <has_size value="0"/>

3:746b434c8fbb

<tool id='usher' name='UShER' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.01'>
    <description>ultrafast sample placement on existing trees</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro='requirements' />
    <version_command>usher --version</version_command>
    <command detect_errors='exit_code'><![CDATA[
        #if $vcf.ext == 'vcf_bgzip':
            ln -s '$vcf' input.vcf.gz &&

        #end if
        $output_options.write_parsimony_scores_per_node
        #if $output_options.multiple_placements
            -M $output_options.multiple_placements
        #end if
        $retain_input_branch_lengths
        -T \${GALAXY_SLOTS:-1}
        -d ./
        #if $output_options.write_subtrees_size
            && mkdir -p out_subtrees out_subtrees_expanded out_subtrees_mutations
            && mv subtree*expanded.txt ./out_subtrees_expanded

            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="vcf" value="new_samples.vcf.gz" ftype="vcf_bgzip"/>
            <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
            <param name="retain_input_branch_lengths" value="true"/>
            <output name="final_tree" file="test_12_final_tree.nh" ftype="newick" lines_diff="2"/>
            <output name="mutation_paths" file="test_12_mutation_path.nh" ftype="txt"/>
            <output name="clades" ftype="txt">
                <assert_contents>
                    <has_size value="0"/>