Mercurial > repos > peter-waltman > ucsc_cluster_tools2
comparison cluster.tools/ipl.feature.selection.xml @ 0:0decf3fd54bc draft
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author | peter-waltman |
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date | Thu, 28 Feb 2013 01:45:39 -0500 |
parents | |
children | dddfeedb85af |
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-1:000000000000 | 0:0decf3fd54bc |
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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> |