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1 <tool id="SAINT_ProteinInteractions_v2" name="SAINT Output to Protein Interaction File">
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2 <description></description>
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3 <command interpreter="python">ProteinInteractions_v2.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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18
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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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18
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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 **Protein Interactions**
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43
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44 This program will read in a SAINT 'list.txt' file and the interactions from ConsensusPathDB ( http://consensuspathdb.org/ ) and return all the interactions that we saw in our experiment in a format suitable for cytoscape. This allows us to filter before getting protein-protein interactions (PPI's) so that it doesn't affect our SAINT score or include interactions that don't score well.
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45
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46 INPUT
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47
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48 SAINT Output: SAINTexpress output.
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49
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50 SAINT Score Cutoff: Saint score cutoff for import (between 0 and 1).
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51
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52 Consensus Path Database Score Cutoff: Confidence of PPI from CPDB to include (between 0 and 1).
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53 * low: no filtering
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54 * medium: >0.5
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55 * high: >0.7
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56 * very high: >0.9
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57
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58 Species: Human, Yeast, or Mouse.
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59
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60 </help>
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61 </tool> |
