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annotate cluster_kegg.xml @ 34:f739a296a339

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Update to Miller Lab devshed revision 09dc81dbebc5
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 23 Sep 2013 13:37:19 -0400
parents a631c2f6d913
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1 <tool id="gd_cluster_kegg" name="Cluster KEGG" version="1.0.0">
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2 <description>: Group gene categories connected by shared genes</description>
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3
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4 <command interpreter="python">
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5 #set $ensembltcolmn_arg = int(str($ensembltcolmn)) - 1
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6 cluster_onConnctdComps.py '--input=$input' '--input_columns=${input.dataset.metadata.columns}' '--outfile=$output' '--threshold=$threshold' '--ENSEMBLTcolmn=$ensembltcolmn_arg' '--classClmns=$classclmns'
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7 </command>
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8
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9 <inputs>
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10 <param name="input" type="data" format="tabular" label="Input dataset" />
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11 <param name="ensembltcolmn" type="data_column" data_ref="input" numerical="false" label="Column with the ENSEMBL code in the Input dataset" />
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12 <param name="threshold" type="float" value="90" min="0" max="100" label="Threshold to disconnect the nodes" />
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13 <param name="classclmns" size="10" type="text" value="c1,c2" label="Gene category columns"/>
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14
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15 </inputs>
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16
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17 <outputs>
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18 <data name="output" format="tabular" />
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19 </outputs>
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20
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21 <requirements>
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22 <requirement type="package" version="1.8.1">networkx</requirement>
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23 </requirements>
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24
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25 <help>
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26 **What it does**
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27
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28 The program builds a network of gene categories connected by shared
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29 genes. The edges of this network are weighted based on the number of
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30 genes that each node shares. The clustering coefficient, c\ :sub:`u`\ , is then calculated for each node using the formula:
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32 .. image:: $PATH_TO_IMAGES/cluster_kegg_formula.png
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33
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34 |
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36 where deg(u) is the degree of u and edge weights, w\ :sub:`uv`\ ,
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37 are normalized by the maximum weight in the network. The cluster
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38 coefficients are then filtered by our program based on threshold (that
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39 could be a percentile or a value choose by the user) and all the nodes
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40 with a cluster coefficient lower than this threshold are deleted from
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41 the network. Finally, the program reports each connected component as
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42 a cluster of gene classifications. With our program a lower number of
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43 gene categories is obtained, but the results are easier to interpret as
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44 they exclude genes present in many gene groups.
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45 </help>
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46 </tool>