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

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

<tool id="FROGS_Core_Main" name="FROGS Core 1-Main" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="24.0">
    <description>ASV reconstruction and taxonomic affiliation</description>
    <macros>
        <import>frogs_core_macros.xml</import>
        <import>processing_short_reads_macros.xml</import>
        <import>processing_long_reads_macros.xml</import>
        <import>processing_454_reads_macros.xml</import>
        <import>remove_chimera_macros.xml</import>
        <import>cluster_filters_macros.xml</import>
        <import>taxonomic_affiliation_macros.xml</import>
        <import>tree_macros.xml</import>
        <import>itsx_macros.xml</import>
    </macros>

    <expand macro="frogs_core_requirements" />

    <command detect_errors="exit_code"><![CDATA[
        ## MAIN TOOLS
        #if $frogs_core_tools.tool_name == "processing_short_reads":
            @PROCESSING_SHORT_READS_CMD_LINE@

        #elif $frogs_core_tools.tool_name == "processing_long_reads":
            @PROCESSING_LONG_READS_CMD_LINE@

        #elif $frogs_core_tools.tool_name == "processing_454_reads":
            @PROCESSING_454_READS_CMD_LINE@

        #elif $frogs_core_tools.tool_name == "remove_chimera":
            @REMOVE_CHIMERA_CMD_LINE@

        #elif $frogs_core_tools.tool_name == "cluster_filters":
            @CLUSTER_FILTERS_CMD_LINE@

        #elif $frogs_core_tools.tool_name == "taxonomic_affiliation":
            @TAXONOMIC_AFFILIATION_CMD_LINE@

        #elif $frogs_core_tools.tool_name == "tree":
            @TREE_CMD_LINE@

        #elif $frogs_core_tools.tool_name == "itsx":
            @ITSX_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="processing_short_reads">1.a. Reads processing of short reads</option> 
                <option value="processing_long_reads">1.b. Reads processing of long reads</option> 
                <option value="processing_454_reads">1.c. Reads processing of 454 reads</option> 
                <option value="remove_chimera">2. Remove chimera</option> 
                <option value="cluster_filters">3. Cluster/ASV filters</option> 
                <option value="taxonomic_affiliation">4. Taxonomic affiliation</option> 
                <option value="tree">5. Phylogenetic tree building</option> 
                <option value="itsx">ITSx</option>               
            </param>
            <when value=""/>
            <!-- ##################### processing_short_reads  ##################### -->
            <when value="processing_short_reads">
                <expand macro="processing_short_reads_inputs" />
            </when>
            <!-- ##################### processing_long_reads  ##################### -->
            <when value="processing_long_reads">
                <expand macro="processing_long_reads_inputs" />
            </when>
            <!-- ##################### processing_454_reads  ##################### -->
            <when value="processing_454_reads">
                <expand macro="processing_454_reads_inputs" />
            </when>
            <!-- ##################### remove_chimera  ##################### -->
            <when value="remove_chimera">
                <expand macro="remove_chimera_inputs" />
            </when>
            <!-- ##################### cluster_filters  ##################### -->
            <when value="cluster_filters">
                <expand macro="cluster_filters_inputs" />
            </when>
            <!-- ##################### taxonomic_affiliation  ##################### -->
            <when value="taxonomic_affiliation">
                <expand macro="taxonomic_affiliation_inputs" />
            </when>
            <!-- ##################### tree  ##################### -->
            <when value="tree">
                <expand macro="tree_inputs" />
            </when>
            <!-- ##################### itsx  ##################### -->
            <when value="itsx">
                <expand macro="itsx_inputs" />
            </when>
        </conditional>
    </inputs>
    
    <outputs>
        <expand macro="frogs_core_outputs" />
    </outputs>
    
    <tests>
        <!-- ##################### 1 processing_short_reads : swarm ##################### -->
        <test expect_num_outputs="4">
            <conditional name="frogs_core_tools">
                <param name="tool_name" value="processing_short_reads"/>
                <expand macro="swarm_processing_short_reads_test_input"/>
            </conditional>
            <expand macro="swarm_processing_short_reads_test_output"/>
        </test>
        <!-- ##################### 2 processing_short_reads : dada2 ##################### -->
        <test expect_num_outputs="3">
            <conditional name="frogs_core_tools">
                <param name="tool_name" value="processing_short_reads"/>
                <expand macro="dada2_processing_short_reads_test_input"/>
            </conditional>
            <expand macro="dada2_processing_short_reads_test_output"/>
        </test>
        <!-- ##################### 3 processing_long_reads : swarm ##################### -->
        <test expect_num_outputs="4">
            <conditional name="frogs_core_tools">
                <param name="tool_name" value="processing_long_reads"/>
                <expand macro="swarm_processing_long_reads_test_input"/>
            </conditional>
            <expand macro="swarm_processing_long_reads_test_output"/>
        </test>
        <!-- ##################### 4 processing_long_reads : dada2 ##################### -->
        <test expect_num_outputs="3">
            <conditional name="frogs_core_tools">
                <param name="tool_name" value="processing_long_reads"/>
                <expand macro="dada2_processing_long_reads_test_input"/>
            </conditional>
            <expand macro="dada2_processing_long_reads_test_output"/>
        </test>
        <!-- ##################### 5 processing_454_reads : swarm ##################### -->
        <test expect_num_outputs="4">
            <conditional name="frogs_core_tools">
                <param name="tool_name" value="processing_454_reads"/>
                <expand macro="swarm_processing_454_reads_test_input"/>
            </conditional>
            <expand macro="swarm_processing_454_reads_test_output"/>
        </test>
        <!-- ##################### 6 remove_chimera ##################### -->
        <test expect_num_outputs="3">
            <conditional name="frogs_core_tools">
                <param name="tool_name" value="remove_chimera"/>
                <expand macro="remove_chimera_test_input"/>
            </conditional>
            <expand macro="remove_chimera_test_output"/>
        </test>
        <!-- ##################### 7 cluster_filters ##################### -->
        <test expect_num_outputs="4">
            <conditional name="frogs_core_tools">
                <param name="tool_name" value="cluster_filters"/>
                <expand macro="cluster_filters_test_input"/>
            </conditional>
            <expand macro="cluster_filters_test_output"/>
        </test>
        <!-- ##################### 8 taxonomic_affiliation ##################### -->
        <test expect_num_outputs="2">
            <conditional name="frogs_core_tools">
                <param name="tool_name" value="taxonomic_affiliation"/>
                <expand macro="taxonomic_affiliation_test_input"/>
            </conditional>
            <expand macro="taxonomic_affiliation_test_output"/>
        </test>
        <!-- ##################### 9 tree ##################### -->
        <test expect_num_outputs="2">
            <conditional name="frogs_core_tools">
                <param name="tool_name" value="tree"/>
                <expand macro="tree_test_input"/>
            </conditional>
            <expand macro="tree_test_output"/>
        </test>
        <!-- ##################### 11 itsx ##################### -->
        <test expect_num_outputs="4">
            <conditional name="frogs_core_tools">
                <param name="tool_name" value="itsx"/>
                <expand macro="itsx_test_input"/>
            </conditional>
            <expand macro="itsx_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>