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1 <tool id="network_attributes" name="Calculate Network Attributes">
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2 <description></description>
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3 <command interpreter="python">Calculate_attributes_wrapper.py $edges $centrality $modularity $node_attr \$INSTALL_RUN_PATH/</command>
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4 <requirements>
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5 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
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6 </requirements>
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7 <inputs>
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8 <param format="sif" name="edges" type="data" label="Network File"/>
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9 <param type="select" name="centrality" label="Select Centrality Metric"/>
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10 <option value="eigenvector">eigenvector centrality</option>
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11 <option value="betweenness">betweenness centrality</option>
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12 <option value="closeness">closeness centrality</option>
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13 <option value="PageRank">Page Rank</option>
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14 <param type="select" name="modularity" label="Select Community Detection Algorithm">
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15 <option value="fast.greedy">Fast Greedy (recommended)</option>
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16 <option value="optimal">Optimal (see note)</option>
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17 <option value="edge.betweenness">Edge Betweenness</option>
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18 <option value="walk.trap">Walk Trap</option>
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19 <option value="spin.glass">Spin Glass</option>
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20 <option value="leading eigenvector">Leading Eigenvector</option>
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21 <option value="label.propagation">Label Propagation</option>
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22 <option value="multilevel">Multilevel</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="txt" name="Node_attributes" label="Node Attributes"/>
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27 </outputs>
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28 <stdio>
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29 <regex match="Error|error"
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30 source="stdout"
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31 level="fatal"
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32 description="Unknown error"/>
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33 <regex match="Error|error"
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34 source="stderr"
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35 level="fatal"
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36 description="Unknown error"/>
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37 </stdio>
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38
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39 <tests>
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40 <test>
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41 <param name="input" value="fa_gc_content_input.fa"/>
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42 <output name="out_file1" file="fa_gc_content_output.txt"/>
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43 </test>
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44 </tests>
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45 <help>
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46 SAINT Output to Protein Interaction File
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47 ----------------------------------------
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48
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49 This tool reads in a network sif file and calculates the specified centrality
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50 metric and perform community detection based on the specified algorithm.
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51
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52 **1) Network File **
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53 This file must be a two column sif file (tab delimited)
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54 e.g. EGFR\_HUMAN GRB2\_HUMAN
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55
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56 **2) Centrality**
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57 Specify centrality metric measuring influence or bottlenecks in the network
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58
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59 **3) Modularity**
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60 Please specify community detection algorithm.
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61 **NOTE:** Optimal community detection computational time scales exponentially
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62 with the number of nodes. Use with caution if number of nodes > 30.
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63 </help>
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64 </tool>
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