sc3-sc3-estimate-k.xml

<tool id="sc3-sc3-estimate-k" name="SC3 estimate k" version="0.1.0">
    <description>Estimate the best K for clustering</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        sc3-sc3-estimate-k.R -i "$input1" -t "$output1" -o R_scater_qc.rds 
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="rds" />
    </inputs>
    <outputs>
        <data name="output1" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="R_sc3_transformed.rds"/>
            <output name="output1" file="sc3-estimated-k.txt"/>
        </test>
    </tests>
    <help><![CDATA[
        Usage: /Users/ct5/anaconda3/envs/galaxy/bin/sc3-sc3-estimate-k.R [options]


Options:
	-i INPUT-OBJECT-FILE, --input-object-file=INPUT-OBJECT-FILE
		File name in which a processed SC3 object can be found.

	-o OUTPUT-OBJECT-FILE, --output-object-file=OUTPUT-OBJECT-FILE
		File name in which to store the SingleCellExperiment object with estimated k'.

	-t OUTPUT-TEXT-FILE, --output-text-file=OUTPUT-TEXT-FILE
		Text file name in which to store the estimated k'.

	-h, --help
		Show this help message and exit



    ]]></help>
    <expand macro="citations" />
</tool>