annotate FROGS_FUNC.xml @ 0:c5fd7b97c2a4 draft default tip

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 78ca62b54aee22893d278d9c3d495527be405f8a

<tool id="FROGS_Func" name="FROGS Func" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="24.0">
    <description>Prediction of functional abundances using marker gene sequences</description>
    <macros>
        <import>frogs_func_macros.xml</import>
        <import>picrust2_placeseq_and_copynumber_macros.xml</import>
        <import>picrust2_functions_macros.xml</import>
        <import>picrust2_pathways_macros.xml</import>
    </macros>

    <expand macro="frogs_func_requirements" />

    <command detect_errors="exit_code"><![CDATA[
        #if $frogs_func_tools.tool_name == "picrust2_placeseq_and_copynumber"
            @PICRUST2_PLACESEQ_AND_COPYNUMBER_CMD_LINE@

        #elif $frogs_func_tools.tool_name == "picrust2_functions"
            @PICRUST2_FUNCTIONS_CMD_LINE@

        #elif $frogs_func_tools.tool_name == "picrust2_pathways"
            @PICRUST2_PATHWAYS_CMD_LINE@
        #end if
    ]]>
    </command>
    
    <inputs>
        <conditional name="frogs_func_tools">
            <param name="tool_name" type="select" display="radio" label="Select a tool from the FROGS Func suite to run your analysis.">
                <option value="" selected="true">-- Please select a tool --</option>
                <option value="picrust2_placeseq_and_copynumber"> Tool 1: sequence placement and gene copy number estimation (PICRUSt2)</option>
                <option value="picrust2_functions">Tool 2: functional abundance estimation (PICRUSt2)</option>
                <option value="picrust2_pathways">Tool 3: pathway abundance estimation (PICRUSt2)</option>
            </param>
            <when value=""/>
            <!-- ##################### picrust2_placeseq_and_copynumber  ##################### -->
            <when value="picrust2_placeseq_and_copynumber">
                <expand macro="picrust2_placeseq_and_copynumber_inputs" />
            </when>
            <!-- ##################### picrust2_functions  ##################### -->
            <when value="picrust2_functions">
                <expand macro="picrust2_functions_inputs" />
            </when>
            <!-- ##################### picrust2_pathways  ##################### -->
            <when value="picrust2_pathways">
                <expand macro="picrust2_pathways_inputs" />
            </when>
        </conditional>
    </inputs>
    
    <outputs>
        <expand macro="frogs_func_outputs" />
    </outputs>
    
    <tests>
        <!-- ##################### 1 picrust2_placeseq_and_copynumber ##################### -->
        <test expect_num_outputs="7">
            <conditional name="frogs_func_tools">
                <param name="tool_name" value="picrust2_placeseq_and_copynumber"/>
                <expand macro="picrust2_placeseq_and_copynumber_test_input"/>
            </conditional>
            <expand macro="picrust2_placeseq_and_copynumber_test_output"/>
        </test>
        <!-- ##################### 2 picrust2_functions ##################### -->
        <test expect_num_outputs="8">
            <conditional name="frogs_func_tools">
                <param name="tool_name" value="picrust2_functions"/>
                <expand macro="picrust2_functions_test_input"/>
            </conditional>
            <expand macro="picrust2_functions_test_output"/>
        </test>        
        <!-- ##################### 3 picrust2_pathways ##################### -->
        <test expect_num_outputs="2">
            <conditional name="frogs_func_tools">
                <param name="tool_name" value="picrust2_pathways"/>
                <expand macro="picrust2_pathways_test_input"/>
            </conditional>
            <expand macro="picrust2_pathways_test_output"/>
        </test>    
    </tests>

    <help><![CDATA[
    For more information and detailed documentation, visit the FROGS website https://frogs.inrae.fr.
    ]]>
    </help>

    <citations>
        <citation type="doi">10.1093/bioinformatics/btx791</citation>
        <citation type="doi">10.1093/bib/bbab318</citation>
    </citations>

</tool>