annotate galaxy/tools/concatenator/concatenator.xml @ 9:728c6b81b45e draft default tip

New Concatenator

<tool id="concatenator" name="Concatenator" version="1.0.0">
    <description>creates a list of accessions and the associated path to their variant calls</description>
    <requirements>
        <requirement type="package" version="0.3">pathogist</requirement>
    </requirements>

    <command><![CDATA[
        $__tool_directory__/concatenator

        #if $input_type.input_type_selector == "variant"
            variant
            -n #for $path in $input_type.paths# ${path.element_identifier} #end for#
            -i #for $path in $input_type.paths# $path #end for#
        #elif $input_type.input_type_selector == "clustering"
            cluster
            #if $input_type.mlst.mlst_checkbox
                --mlst $input_type.mlst.mlst_path
            #end if
            #if $input_type.snp.snp_checkbox
                --snp $input_type.snp.snp_path
            #end if
            #if $input_type.cnv.cnv_checkbox
                --cnv $input_type.cnv.cnv_path
            #end if
            #if $input_type.spoligo.spoligo_checkbox
                --spoligo $input_type.spoligo.spoligo_path
            #end if
         #elif $input_type.input_type_selector == "reads"
            reads
            $input_type.fastq.forward
            $input_type.fastq.reverse
         #end if
    ]]></command>


    <inputs>
        <conditional name="input_type">
            <param name="input_type_selector" type="select" label="Concatenation of variant calls, or clustering files">
                <option value="variant">Variant Call Files</option>
                <option value="clustering">Clustering/Distance Matrix Files</option>
                <option value="reads">Raw reads</option>
            </param>
            <when value="variant">
                <param name="paths" type="data" label="Collection of calls" help="" optional="False" multiple="True"/>
            </when>
            <when value="clustering">
                <conditional name="mlst">
                    <param name="mlst_checkbox" type="boolean" label="Include MLST"/>
                    <when value="true">
                        <param name="mlst_path" type="data" label="MLST Clustering/Distance Matrix file"
                               format="txt,tabular"/>
                    </when>
                </conditional>
                <conditional name="snp">
                    <param name="snp_checkbox" type="boolean" label="Include SNP"/>
                    <when value="true">
                        <param name="snp_path" type="data" label="SNP Clustering/Distance Matrix file"
                               format="txt,tabular"/>
                    </when>
                </conditional>
                <conditional name="cnv">
                    <param name="cnv_checkbox" type="boolean" label="Include CNV"/>
                    <when value="true">
                        <param name="cnv_path" type="data" label="CNV Clustering/Distance Matrix file"
                               format="txt,tabular"/>
                    </when>
                </conditional>
                <conditional name="spoligo">
                    <param name="spoligo_checkbox" type="boolean" label="Include Spoligotyping"/>
                    <when value="true">
                        <param name="spoligo_path" type="data" label="Spoligotyping Clustering/Distance Matrix file"
                               format="txt,tabular"/>
                    </when>
                </conditional>
            </when>
            <when value="reads">
                <param name="fastq" type="data_collection" collection_type="paired"
                       format="fastqsanger,fastq,fastq.gz,fastqsanger.gz" label="Select paired collection"/>
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data name="output" label="Paths of ${on_string}" format="txt" from_work_dir="paths.txt">
            <filter>input_type[input_type_selector] == 'variant'
                or input_type[input_type_selector] == 'clustering'</filter>
        </data>
        <data name="forward" label="Paths of ${on_string} (forward reads)" format="txt" from_work_dir="forward.txt">
            <filter>input_type[input_type_selector] == 'reads'</filter>
        </data>
        <data name="reverse" label="Paths of ${on_string} (reverse reads)" format="txt" from_work_dir="reverse.txt">
            <filter>input_type[input_type_selector] == 'reads'</filter>
        </data>
    </outputs>

    <help>

    </help>

    <citations>

    </citations>
</tool>