comparison Marea/marea.xml @ 28:e6831924df01 draft

small fixes (elbow plot and output managment)

27:8c480c977a12

            #end for
        #elif $cond.type_selector == 'dataset_class':
            --input_data ${input_data}
            --input_class ${input_class}
        #end if
        ]]>
    </command>

    <inputs>
        <conditional name="cond_rule">

        </conditional>
        <conditional name="cond">
            <param name="type_selector" argument="--option" type="select" label="Input format:">
                <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N</option>
                <option value="dataset_class">RNAseq of all samples + sample group specification</option>
            </param>
            <when value="datasets">
                <repeat name="input_Datasets" title="RNAseq" min="2">
                    <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />	
                    <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
                </repeat>
            </when>
            <when value="dataset_class">
                <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
                <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
            </when>
        </conditional>
       
	<conditional name="advanced">
		<param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom rules for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps.">
		    <option value="true" selected="true">No</option>
		    <option value="false">Yes</option>

    	</conditional>
    </inputs>

    <outputs>
        <data format="txt" name="log" label="${tool.name} - Log" />
        <collection name="results" type="list" label="${tool.name} - Results">
            <discover_datasets pattern="__name_and_ext__" directory="result"/>
        </collection>
	<collection name="ras" type="list" label="${tool.name} - RAS" format_source="tabular">
	    <filter>advanced['choice'] and advanced['generateRas']</filter>
    	    <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/>
	</collection>
    </outputs>
    <tests>
        <test>
            <param name="pValue" value="0.56"/>
            <output name="log" file="log.txt"/>

28:e6831924df01

            #end for
        #elif $cond.type_selector == 'dataset_class':
            --input_data ${input_data}
            --input_class ${input_class}
        #end if
        #if $cond.type_selector == 'datasets_rasonly':
            --input_datas ${input_Datasets}
            --single_ras_file $ras_single
        #end if
        ]]>
    </command>

    <inputs>
        <conditional name="cond_rule">

        </conditional>
        <conditional name="cond">
            <param name="type_selector" argument="--option" type="select" label="Input format:">
                <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N</option>
                <option value="dataset_class">RNAseq of all samples + sample group specification</option>
                <option value="datasets_rasonly" selected="true">RNAseq dataset</option>
            </param>
            <when value="datasets">
                <repeat name="input_Datasets" title="RNAseq" min="2">
                    <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />	
                    <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
                </repeat>
            </when>
            <when value="datasets_rasonly">
                <param name="input_Datasets" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
            </when>
            <when value="dataset_class">
                <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
                <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
            </when>
        </conditional>
       
       
       <!--TODO: NASCONDERE ADVANCED SE RAS ONLY-->
       
	<conditional name="advanced">
		<param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom rules for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps.">
		    <option value="true" selected="true">No</option>
		    <option value="false">Yes</option>

    	</conditional>
    </inputs>

    <outputs>
        <data format="txt" name="log" label="${tool.name} - Log" />
        <data format="tabular" name="ras_single" label="${tool.name} - RAS">
        	<filter>cond['type_selector'] == "datasets_rasonly"</filter>
        </data>
        <collection name="results" type="list" label="${tool.name} - Results">
        <filter>cond['type_selector'] == "datasets" or cond['type_selector'] == "dataset_class"</filter>
            <discover_datasets pattern="__name_and_ext__" directory="result"/>
        </collection>
	<collection name="ras" type="list" label="${tool.name} - RAS list" format_source="tabular">
	    <filter>advanced['choice'] and advanced['generateRas']</filter>
    	    <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/>
	</collection>
	
    </outputs>
    <tests>
        <test>
            <param name="pValue" value="0.56"/>
            <output name="log" file="log.txt"/>