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1 <tool id="determine_ipl_threshold" name="Determine IPL Threshold for Consensus Clustering" force_history_refresh="True">
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2 <command interpreter="python">determine.IPL.threshold.py
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3 -d ${data_fname}
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4 -f ${filter_type}
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5 -p ${percentage_pass}
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6 -s ${selection_criteria}
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7 -h $report
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8 -r ${report.files_path}
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9 -o ${output_rdata}
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10 </command>
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11 <inputs>
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12 <param name="data_fname" type="data" format="tabular" label="Paradigm Results File (contains both reals and nulls)"/>
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13 <param name="filter_type" type="select" label="Activity Filter" help="Specify the filter type to use (see help below)">
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14 <option value="active">Active</option>
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15 <option value="inactive">Inactive</option>
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16 <option value="modulated" selected='true' >Modulated</option>
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17 </param>
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18 <param name="percentage_pass" type="float" label="% of Samples Passing (value in 0-1 range; >= 1 to indicate exact number of samples)" value="0.33" help="Specify the percentage of samples thatmust pass the threshold (see help below)"/>
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19 <param name="selection_criteria" type="select" label="Selection Criteria" help="Specify the test statistic to use to select the threshold (see help below)">
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20 <option value="binomial">Binomial P-value</option>
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21 <option value="chisq">Chi-Squared P-value</option>
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22 <option value="max_diffs" selected='true' >Overall Max Number of Differences</option>
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23 </param>
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24 </inputs>
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25 <outputs>
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26 <data format="html" name="report" label="Determine IPL Threshold (HTML)"/>
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27 <data format="rdata" name="output_rdata" label="Determine IPL Threshold (RData)"/>
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28 </outputs>
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29 <help>
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30
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31 .. class:: infomark
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32
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33 **Determines a statistically sound threshold to use for a given IPL result**
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34
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35 **Parameters**
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36 - **Paradigm Results File** Output from Paradigm (tab-delimited and contains both the 'real' and 'null' samples)
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37
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38 - **Activity Filter** Specify the filter type to use. Choice of:
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39
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40 * Activity - Features must exceed the user-specified threshold
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41 * Inactivity - Features must fall below the user-specified threshold
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42 * Modulated - Absolute value of the features must exceed the specified threshold
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43
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44 - **Percentage of Samples Passing** Percent of samples with an IPL that passes the threshold. Choice of:
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45
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46 * Real Value in [0,1] - indicate the percentage of samples that pass the threshold
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47 * Integer Value - indicate the exact number of samples that pass the threshold
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48
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49 - **Selection Criteria** Specify the test statistic to use to select the threshold. Choice of:
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50
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51 * Binomial P-value - Select the threshold with the largest -log p-value (calculated as a binomial)
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52 * Chi-Squared P-value - Select the threshold with the largest -log p-value (calculated as a Chi-squared)
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53 * Overall Max Number of Differences - Select the threshold with the largest overall number of differences between the real and null distributions
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54
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55
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56 </help>
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57 </tool>
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