comparison cluster.tools/ipl.feature.selection.xml @ 0:0decf3fd54bc draft

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author peter-waltman
date Thu, 28 Feb 2013 01:45:39 -0500
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children dddfeedb85af
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-1:000000000000 0:0decf3fd54bc
1 <tool id="ipl_feature_selection" name="IPL Feature Selection" force_history_refresh="True">
2 <command interpreter="python">ipl.feature.selection.py
3 -d $dataset
4 ${genes_only}
5 -o ${output}
6
7 #if str($thresh_format.format) == 'manual':
8 -f ${thresh_format.filter}
9 -t ${thresh_format.threshold}
10 -p ${thresh_format.perc_pass}
11 #end if
12 #if str($thresh_format.format) == 'empirical':
13 -e ${empirical_fname}
14 #end if
15
16 </command>
17 <inputs>
18 <param name="dataset" type="data" format='tabular' label="Data Set"/>
19 <param name="genes_only" type="boolean" label="Genes Only (check to set yes)" truevalue="-g" falsevalue="" checked="False" />
20
21 <conditional name="thresh_format" >
22 <param name="format" type='select' label="Input Format for Threshold Used" >
23 <option value="empirical" selected='true'>Output from the Determine Threshold Tool</option>
24 <option value="manual">Manually Specify the Threshold</option>
25 </param>
26 <when value="manual" >
27 <param name="filter" type="select" label="Activity Filter" >
28 <option value="modulated" select='true' >Modulated</option>
29 <option value="active">Active</option>
30 <option value="inactive">Inactive</option>
31 </param>
32 <param name="perc_pass" type="float" label="% of Samples Passing (value in 0-1 range; >= 1 to indicate exact number of samples)" value="0.33"/>
33 <param name="threshold" type="float" label="Activity Threshold" value="0.25"/>
34 </when>
35 <when value="empirical" >
36 <param name="empirical_fname" type="data" format='rdata' label="Activity Threshold File" />
37 </when>
38 </conditional>
39 </inputs>
40 <outputs>
41 <data format="tabular" name="output" label="Filtered IPLs"/>
42 </outputs>
43 <help>
44 .. class:: infomark
45
46 **IPL Feature Selection** - Tool to filter an IPL matrix to contain only those features that exceed a given threshold for a specified percentage of samples
47
48 **OUTPUT:** A new matrix containing only the feaures that pass the user-specified filter
49
50 ----
51
52 **Parameters**
53
54 - **Genes Only** Check to limit the new matrix to only gene features
55
56 - **Input Format for Threshold Used:** - Specify the format to specify the Threshold. Choice of:
57 * Output from the 'Determine Threshold Tool'
58 * Manually Specify the Threshold
59
60 - **IF Output from the 'Determine Threshold Tool' IS SELECTED:**
61 * **Activity Threshold File** Specify the result file from the 'Determine IPL Threshold for Consensus Clustering" tool
62
63 - **IF Manually Specify the Threshold IS SELECTED:**
64 * **Activity Filter** Specify the filter type to use. Choice of:
65
66 * Activity - Features must exceed the user-specified threshold
67 * Inactivity - Features must fall below the user-specified threshold
68 * Modulated - Absolute value of the features must exceed the specified threshold
69
70 * **Percentage of Samples Passing** Percent of samples with an IPL that passes the threshold. Choice of:
71
72 * Real Value in [0,1] - indicate the percentage of samples that pass the threshold
73 * Integer Value - indicate the exact number of samples that pass the threshold
74
75 * **Selection Criteria** Specify the test statistic to use to select the threshold. Choice of:
76
77 * Binomial P-value - Select the threshold with the largest -log p-value (calculated as a binomial)
78 * Chi-Squared P-value - Select the threshold with the largest -log p-value (calculated as a Chi-squared)
79 * Overall Max Number of Differences - Select the threshold with the largest overall number of differences between the real and null distributions
80
81
82 </help>
83 </tool>