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1 <?xml version='1.1' encoding='utf-8'?>
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2 <tool id="Matrix_Filters" name="Matrix Filters" version="2.1.12">
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3 <description> rows or columns based on specified threshold</description>
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4 <command interpreter="python">Matrix_Filters.py '$p_input' '$extra.choice' '$extra.thresh' '$axes' '$output_file'</command>
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5 <inputs>
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6 <param name="p_input" type="data" format="tabular" label="Input Matrix" />
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7
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8 <conditional name="extra">
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9 <param name="choice" type="select" label="Choose Metric to Filter By">
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10 <option value="LowerLimit">Remove row/column if any cell is less than threshold value</option>
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11 <option value="UpperLimit">Remove row/column if any cell is greater than threshold value</option>
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12 <option value="NANnumber">Remove row/column if number NAN cells exceeds threshold value </option>
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13 <option value="NANpercent">Remove row/column if NAN cells exceeds threshold percent</option>
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14 <option value="VarianceValue">Remove row/column if Variance is below threshold value</option>
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15 <option value="VarianceCount">Remove row/column if Variance is not in top row/column count</option>
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16 <option value="VariancePercent">Remove row/column if Variance is not in top percent</option>
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17 <option value="MADcount">Remove row/column if Median Absolute Deviation (MAD) is not in top row/column count</option>
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18 <option value="MADpercent">Remove row/column if Median Absolute Deviation (MAD) is not in top percent</option>
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19 <!-- <option value="Covariance">Remove row/column if covariance exceeds threshold value</option>
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20 <option value="Median">Remove row/column if Median is less than threshold value</option>
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21 <option value="MADvalue">Remove row/column if Median Absolute Deviation (MAD) is below threshold value</option>
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22 <option value="Mean">Remove row/column if Mean is less than threshold value</option>
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23 <option value="Quantile">Remove row/column if less than Quantile_Cutoff</option>
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24 <option value="GeneList">Keep only these genes</option>
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25 <option value="Histogram">View filter histogram</option>
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26 -->
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27 </param>
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28 <when value="LowerLimit">
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29 <param name="thresh" type="float" size="5" value="0.01" label="Absolute minimum value" help="Lowest value allowed or row/col removed."/>
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30 </when>
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31 <when value="UpperLimit">
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32 <param name="thresh" type="float" size="5" value="0.9" label="Absolute maximum value" help="Highest value allowed or row/col removed."/>
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33 </when>
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34 <when value="NANnumber">
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35 <param name="thresh" type="float" size="5" value="50" label="Maximum number NANs" help="More NANs per row/col removed."/>
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36 </when>
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37 <when value="NANpercent">
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38 <param name="thresh" type="float" size="5" value="20" label="Percent maximum" help="Above percent rows/cols removed."/>
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39 </when>
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40 <when value="Variance">
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41 <param name="thresh" type="float" size="5" value="90" label="Percentile minimum" help="Below percentile rows/cols removed."/>
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42 </when>
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43 </conditional>
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44 <!--
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45 <param name="thresh" type="float" size="4" value=".05" label="Filter Threshold (Value above/below row/column will be Removed)" />
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46 -->
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47 <param name="axes" type="select" label="Choose Axes to Filter on (Rows or Columns)">
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48 <option value="Row">Row</option>
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49 <option value="Column">Column</option>
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50 </param>
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51
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52
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53 </inputs>
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54 <outputs>
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55 <data name="output_file" format="tabular" />
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56 </outputs>
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57
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58 </tool> |
