sc3-sc3-calc-biology.xml

<tool id="sc3-sc3-calc-biology" name="SC3 calculate biology" version="0.1.0">
    <description>SC3 calculates biologically relevant clusters</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        sc3-sc3-calc-biology.R -i "$input1" -o "$output1"
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="rds" />
    </inputs>
    <outputs>
        <data name="output1" format="rds" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="R_sc3_kmeans.rds"/>
            <output name="output1" file="R_sc3_kmeans_biology.rds"/>
        </test>
    </tests>
    <help><![CDATA[
        Usage: /Users/ct5/anaconda3/envs/galaxy/bin/sc3-sc3-calc-biology.R [options]


Options:
	-i INPUT-OBJECT-FILE, --input-object-file=INPUT-OBJECT-FILE
		File name in which a SC3 'SingleCellExperiment' object has been stored after kmeans clustering.

	-d OUTPUT-DIR, --output-dir=OUTPUT-DIR
		An output directory in which to write k-wise outputs.

	-k KS, --ks=KS
		A comma-separated string or single value representing the number of clusters k to be used for SC3 clustering.

	-r REGIME, --regime=REGIME
		defines what biological analysis to perform. "marker" for marker genes, "de" for differentiall expressed genes and "outl" for outlier cells.

	-o OUTPUT-OBJECT-FILE, --output-object-file=OUTPUT-OBJECT-FILE
		File name for R object of type 'SingleCellExperiment' from SC3 in which to store the consensus matrix.

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


Error in wsc_parse_args(option_list, mandatory = c("input_object_file",  : 
  Mandatory argment 'input_object_file' not supplied
Execution halted

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