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1 <tool id="SAINT_ProteinInteractions" name="SAINT Output to Protein Interaction File">
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2 <description></description>
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3 <command interpreter="python">ProteinInteractions.py $input $saint_cutoff $CPDB_cutoff $species $Cytoscape_File \$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="txt" name="input" type="data" label="SAINT Output"/>
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9 <param type="float" name="saint_cutoff" label="Saint Score Cutoff" value="0.8"/>
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10 <param type="float" name="CPDB_cutoff" label="Consensus Path Database Score Cutoff" value="0.8"/>
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11 <param type="select" name="species" label="Species">
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12 <option value="Human">Human</option>
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13 <option value="Yeast">Yeast</option>
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14 <option value="Mouse">Mouse</option>
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15 </param>
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16 </inputs>
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17 <outputs>
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18 <data format="sif" name="Cytoscape_File" label="Cytoscape File"/>
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19 </outputs>
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20 <stdio>
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21 <regex match="Error|error"
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22 source="stdout"
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23 level="fatal"
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24 description="Unknown error"/>
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25 <regex match="Error|error"
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26 source="stderr"
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27 level="fatal"
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28 description="Unknown error"/>
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29 <regex match="Error: bad bait"
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30 source="stdout"
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31 level="fatal"
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32 description="Error: bad bait"/>
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33 </stdio>
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34
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35 <tests>
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36 <test>
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37 <param name="input" value="fa_gc_content_input.fa"/>
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38 <output name="out_file1" file="fa_gc_content_output.txt"/>
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39 </test>
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40 </tests>
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41 <help>
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42 SAINT Output to Protein Interaction File
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43 ----------------------------------------
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44
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45 This tool reads in a *list.txt* file from SAINTexpress and the
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46 interactions from ConsensusPathDB (http://consensuspathdb.org/) and
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47 returns all the known protein-protein interactions observed in the
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48 experiment as a simple interaction file (.SIF).
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49
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50 **Note:** This network will not include identified interactions
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51 between baits and preys. This tool queries known interactions
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52 between preys only
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53
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54 **1) SAINT Output File**
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55
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56 SAINTexpress generated *list.txt* file.
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57
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58 **Note:** Prey IDs must be in Uniprot/Swissprot format (e.g.
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59 "EGFR\_HUMAN" or "P00533").
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60
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61 **2) SAINT Score Cutoff**
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62
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63 SaintScore filter in range 0-1 (default 0.8)
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64
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65 **3) Consensus Path Database Score Cutoff**
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66
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67 Interaction confidence filter in range 0-1 (default 0.8) to specify
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68 which protein interactions in ConsensusPathDB to include.
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69
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70 **4) Species**
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71
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72 Please specify species. Supported species are Human, Mouse, and Yeast.
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73 </help>
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74 </tool> |
