annotate FROGS_CORE_COMPANION.xml @ 2:76ff9af5c0a3 draft default tip

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e987ae3594883fb3b12d2999c6ad7fccd0b1b64

<tool id="FROGS_Core_Companion" name="FROGS Core 2-Companion" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="24.0">
    <description>Optional process, converter, and report</description>
    <macros>
        <import>frogs_core_macros.xml</import>
        <import>demultiplex_macros.xml</import>
        <import>affiliation_filters_macros.xml</import>
        <import>affiliation_postprocess_macros.xml</import>
        <import>normalisation_macros.xml</import>
        <import>biom_to_tsv_macros.xml</import>
        <import>tsv_to_biom_macros.xml</import>
        <import>cluster_asv_report_macros.xml</import>
        <import>affiliation_report_macros.xml</import>
    </macros>

    <expand macro="frogs_core_requirements" />

    <command detect_errors="exit_code"><![CDATA[
        #if $frogs_core_tools.tool_name == "demultiplex":
            @DEMULTIPLEX_CMD_LINE@

        #elif $frogs_core_tools.tool_name == "affiliation_filters":
            @AFFILIATION_FILTERS_CMD_LINE@

        #elif $frogs_core_tools.tool_name == "affiliation_postprocess":
            @AFFILIATION_POSTPROCESS_CMD_LINE@

        #elif $frogs_core_tools.tool_name == "normalisation":
            @NORMALISATION_CMD_LINE@

        #elif $frogs_core_tools.tool_name == "biom_to_tsv":
            @BIOM_TO_TSV_CMD_LINE@

        #elif $frogs_core_tools.tool_name == "tsv_to_biom":
            @TSV_TO_BIOM_CMD_LINE@
            
        #elif $frogs_core_tools.tool_name == "cluster_asv_report":
            @CLUSTER_ASV_REPORT_CMD_LINE@

        #elif $frogs_core_tools.tool_name == "affiliation_report":
            @AFFILIATION_REPORT_CMD_LINE@
        #end if
    ]]>
    </command>
    
    <inputs>
        <conditional name="frogs_core_tools">
            <param name="tool_name" type="select" display="radio" label="Select a tool from the FROGS Core suite to run your analysis.">
                <option value="" selected="true">-- Please select a tool --</option>
                <option value="demultiplex">Read demultiplexing</option> 
                <option value="affiliation_filters">Affiliation filters </option> 
                <option value="affiliation_postprocess">Affiliation postprocessing </option> 
                <option value="normalisation">Abundance normalisation </option> 
                <option value="biom_to_tsv">Convert Biom file to TSV file</option> 
                <option value="tsv_to_biom">Convert TSV file to Biom file</option> 
                <option value="cluster_asv_report">Cluster/ASV report</option> 
                <option value="affiliation_report">Affiliation report</option>                
            </param>
            <when value=""/>
            <!-- ##################### demultiplex  ##################### -->
            <when value="demultiplex">
                <expand macro="demultiplex_inputs" />
            </when>
            <!-- ##################### affiliation_filters  ##################### -->
            <when value="affiliation_filters">
                <expand macro="affiliation_filters_inputs" />
            </when>
            <!-- ##################### affiliation_postprocess  ##################### -->
            <when value="affiliation_postprocess">
                <expand macro="affiliation_postprocess_inputs" />
            </when>
            <!-- ##################### normalisation  ##################### -->
            <when value="normalisation">
                <expand macro="normalisation_inputs" />
            </when>
            <!-- ##################### biom_to_tsv  ##################### -->
            <when value="biom_to_tsv">
                <expand macro="biom_to_tsv_inputs" />
            </when>
            <!-- ##################### tsv_to_biom  ##################### -->
            <when value="tsv_to_biom">
                <expand macro="tsv_to_biom_inputs" />
            </when>
            <!-- ##################### cluster_asv_report  ##################### -->
            <when value="cluster_asv_report">
                <expand macro="cluster_asv_report_inputs" />
            </when>
            <!-- ##################### affiliation_report  ##################### -->
            <when value="affiliation_report">
                <expand macro="affiliation_report_inputs" />
            </when>
        </conditional>
    </inputs>
    
    <outputs>
        <expand macro="frogs_core_outputs" />
    </outputs>
    
    <tests>
        <!-- ##################### 1 demultiplex ##################### -->
        <test expect_num_outputs="3">
            <conditional name="frogs_core_tools">
                <param name="tool_name" value="demultiplex"/>
                <expand macro="demultiplex_test_input"/>
            </conditional>
            <expand macro="demultiplex_test_output"/>
        </test>
        <!-- ##################### 2 affiliation_filters ##################### -->
        <test expect_num_outputs="4">
            <conditional name="frogs_core_tools">
                <param name="tool_name" value="affiliation_filters"/>
                <expand macro="affiliation_filters_test_input"/>
            </conditional>
            <expand macro="affiliation_filters_test_output"/>
        </test>
        <!-- ##################### 3 affiliation_postprocess ##################### -->
        <test expect_num_outputs="3">
            <conditional name="frogs_core_tools">
                <param name="tool_name" value="affiliation_postprocess"/>
                <expand macro="affiliation_postprocess_test_input"/>
            </conditional>
            <expand macro="affiliation_postprocess_test_output"/>
        </test>
        <!-- ##################### 4 normalisation ##################### -->
        <test expect_num_outputs="3">
            <conditional name="frogs_core_tools">
                <param name="tool_name" value="normalisation"/>
                <expand macro="normalisation_test_input"/>
            </conditional>
            <expand macro="normalisation_test_output"/>
        </test>
        <!-- ##################### 5 biom_to_tsv ##################### -->
        <test expect_num_outputs="2">
            <conditional name="frogs_core_tools">
                <param name="tool_name" value="biom_to_tsv"/>
                <expand macro="biom_to_tsv_test_input"/>
            </conditional>
            <expand macro="biom_to_tsv_test_output"/>
        </test> 
        <!-- ##################### 6 tsv_to_biom ##################### -->
        <test expect_num_outputs="2">
            <conditional name="frogs_core_tools">
                <param name="tool_name" value="tsv_to_biom"/>
                <expand macro="tsv_to_biom_test_input"/>
            </conditional>
            <expand macro="tsv_to_biom_test_output"/>
        </test>        
        <!-- ##################### 7 cluster_asv_report ##################### -->
        <test expect_num_outputs="1">
            <conditional name="frogs_core_tools">
                <param name="tool_name" value="cluster_asv_report"/>
                <expand macro="cluster_asv_report_test_input"/>
            </conditional>
            <expand macro="cluster_asv_report_test_output"/>
        </test>   
        <!-- ##################### 8 affiliation_report ##################### -->
        <test expect_num_outputs="1">
            <conditional name="frogs_core_tools">
                <param name="tool_name" value="affiliation_report"/>
                <expand macro="affiliation_report_test_input"/>
            </conditional>
            <expand macro="affiliation_report_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>