Mercurial > repos > md-anderson-bioinformatics > matrix_manipulation
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author | insilico-bob |
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date | Tue, 27 Nov 2018 14:20:40 -0500 |
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<?xml version='1.1' encoding='utf-8'?> <tool id="Matrix_Filters" name="Matrix Filters" version="2.1.12"> <description> rows or columns based on specified threshold</description> <command interpreter="python">Matrix_Filters.py '$p_input' '$extra.choice' '$extra.thresh' '$axes' '$output_file'</command> <inputs> <param name="p_input" type="data" format="tabular" label="Input Matrix" /> <conditional name="extra"> <param name="choice" type="select" label="Choose Metric to Filter By"> <option value="LowerLimit">Remove row/column if any cell is less than threshold value</option> <option value="UpperLimit">Remove row/column if any cell is greater than threshold value</option> <option value="NANnumber">Remove row/column if number NAN cells exceeds threshold value </option> <option value="NANpercent">Remove row/column if NAN cells exceeds threshold percent</option> <option value="VarianceValue">Remove row/column if Variance is below threshold value</option> <option value="VarianceCount">Remove row/column if Variance is not in top row/column count</option> <option value="VariancePercent">Remove row/column if Variance is not in top percent</option> <option value="MADcount">Remove row/column if Median Absolute Deviation (MAD) is not in top row/column count</option> <option value="MADpercent">Remove row/column if Median Absolute Deviation (MAD) is not in top percent</option> <!-- <option value="Covariance">Remove row/column if covariance exceeds threshold value</option> <option value="Median">Remove row/column if Median is less than threshold value</option> <option value="MADvalue">Remove row/column if Median Absolute Deviation (MAD) is below threshold value</option> <option value="Mean">Remove row/column if Mean is less than threshold value</option> <option value="Quantile">Remove row/column if less than Quantile_Cutoff</option> <option value="GeneList">Keep only these genes</option> <option value="Histogram">View filter histogram</option> --> </param> <when value="LowerLimit"> <param name="thresh" type="float" size="5" value="0.01" label="Absolute minimum value" help="Lowest value allowed or row/col removed."/> </when> <when value="UpperLimit"> <param name="thresh" type="float" size="5" value="0.9" label="Absolute maximum value" help="Highest value allowed or row/col removed."/> </when> <when value="NANnumber"> <param name="thresh" type="float" size="5" value="50" label="Maximum number NANs" help="More NANs per row/col removed."/> </when> <when value="NANpercent"> <param name="thresh" type="float" size="5" value="20" label="Percent maximum" help="Above percent rows/cols removed."/> </when> <when value="Variance"> <param name="thresh" type="float" size="5" value="90" label="Percentile minimum" help="Below percentile rows/cols removed."/> </when> </conditional> <!-- <param name="thresh" type="float" size="4" value=".05" label="Filter Threshold (Value above/below row/column will be Removed)" /> --> <param name="axes" type="select" label="Choose Axes to Filter on (Rows or Columns)"> <option value="Row">Row</option> <option value="Column">Column</option> </param> </inputs> <outputs> <data name="output_file" format="tabular" /> </outputs> </tool>