comparison hyphy_annotate.xml @ 14:dd0deea7ac09 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy commit 74395802c1621d4b2a169b3953090ad736f6fc70

13:b315ee3d3487

    <command detect_errors="exit_code"><![CDATA[
        cp '$input_tree' input.nhx &&
        hyphy label-tree
            --tree input.nhx
            --output labeled_tree.nhx
            #if $regexp:
                --regexp '$regexp'
            #else:
                --list '$list_file'
            #end if
            --label '$label'
            --reroot '$reroot'
            '$invert'
            --internal-nodes '$internal_nodes'

    <tests>
        <test expect_num_outputs="2">
            <param name="input_tree" ftype="nhx" value="annotate-in1.nhx"/>
            <conditional name="selection_method">
                <param name="method" value="regexp"/>
                <param name="regexp" value="USA"/>
            </conditional>
            <param name="label" value="Annotated"/>
            <param name="reroot" value="None"/>
            <param name="invert" value="No"/>
            <param name="internal_nodes" value="All descendants"/>
            <param name="leaf_nodes" value="Label"/>
            <output name="labeled_tree" file="annotate-out1-full.nhx" />
            <output name="annotate_md_report">
                <assert_contents>
                    <has_text text="Analysis Description"/>
                </assert_contents>
            </output>
            
        </test>
    </tests>
    <help><![CDATA[
HyPhy Annotate (label-tree)
===========================

14:dd0deea7ac09

    <command detect_errors="exit_code"><![CDATA[
        cp '$input_tree' input.nhx &&
        hyphy label-tree
            --tree input.nhx
            --output labeled_tree.nhx
            #if $selection_method.method == 'regexp':
                --regexp '$selection_method.regexp'
            #else:
                --list '$selection_method.list_file'
            #end if
            --label '$label'
            --reroot '$reroot'
            '$invert'
            --internal-nodes '$internal_nodes'

    <tests>
        <test expect_num_outputs="2">
            <param name="input_tree" ftype="nhx" value="annotate-in1.nhx"/>
            <conditional name="selection_method">
                <param name="method" value="regexp"/>
                <param name="regexp" value="_USA_"/>
            </conditional>
            <param name="label" value="Annotated"/>
            <param name="reroot" value="None"/>
            <param name="invert" value="No"/>
            <param name="internal_nodes" value="All descendants"/>
            <param name="leaf_nodes" value="Label"/>
            <output name="labeled_tree">
                <assert_contents>
                    <has_text text="{Annotated}"/>
                    <has_text text="gb_MW540268"/>
                    <not_has_text text="REFERENCE{Annotated}"/>
                    <not_has_text text="gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND{Annotated}"/>
                </assert_contents>
            </output>
            <output name="annotate_md_report">
                <assert_contents>
                    <has_text text="Analysis Description"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">
            <param name="input_tree" ftype="nhx" value="annotate-in1.nhx"/>
            <conditional name="selection_method">
                <param name="method" value="list"/>
                <param name="list_file" ftype="txt" value="annotate-list1.txt"/>
            </conditional>
            <param name="label" value="Annotated"/>
            <param name="reroot" value="None"/>
            <param name="invert" value="No"/>
            <param name="internal_nodes" value="All descendants"/>
            <param name="leaf_nodes" value="Label"/>
            <output name="labeled_tree">
                <assert_contents>
                    <has_text text="{Annotated}"/>
                    <has_text text="gb_MW540268"/>
                    <not_has_text text="REFERENCE{Annotated}"/>
                </assert_contents>
            </output>
            <output name="annotate_md_report">
                <assert_contents>
                    <has_text text="Analysis Description"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
HyPhy Annotate (label-tree)
===========================