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

New Concatenator

8:7708da43aefb

                --cnv $input_type.cnv.cnv_path
            #end if
            #if $input_type.spoligo.spoligo_checkbox
                --spoligo $input_type.spoligo.spoligo_path
            #end if
         #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>
            </param>
            <when value="variant">
                <param name="paths" type="data" label="Collection of calls" help="" optional="False" multiple="True"/>
            </when>
            <when value="clustering">

                        <param name="spoligo_path" type="data" label="Spoligotyping Clustering/Distance Matrix file"
                               format="txt,tabular"/>
                    </when>
                </conditional>
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data name="output" label="Paths of ${on_string}" format="txt" from_work_dir="paths.txt"/>
    </outputs>

    <help>

    </help>

9:728c6b81b45e

                --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">

                        <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>