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1 <tool id="ProHits_DotPlot_Generator" name="ProHits DotPlot Generator">
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2 <description></description>
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3 <command interpreter="python">ProHits_DotPlot_Generator.py $saint_file $FDR1 $FDR2 $spec_max $dotplot $heatmap $estimated $stats \$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="saint_file" type="data" label="SAINT Output"/>
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9 <param type="float" name="FDR1" label="False Discovery Rate 1" value="0.01"/>
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10 <param type="float" name="FDR2" label="False Discovery Rate 2" value="0.025"/>
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11 <param type="integer" name="spec_max" label="Maximum spectral count" value="50"/>
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12 </inputs>
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13 <outputs>
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14 <data format="pdf" name="dotplot" label="DotPlot" />
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15 <data format="pdf" name="heatmap" label="Heatmap" />
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16 <data format="pdf" name="estimated" label="Estimated" />
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17 <data format="pdf" name="stats" label="Stats" />
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18 </outputs>
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19 <stdio>
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20 <regex match="Error|error"
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21 source="stdout"
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22 level="fatal"
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23 description="Unknown error"/>
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24 <regex match="Error|error"
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25 source="stderr"
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26 level="fatal"
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27 description="Unknown error"/>
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28 <regex match="Error: bad bait"
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29 source="stdout"
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30 level="fatal"
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31 description="Error: bad bait"/>
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32 <regex match="os.rename(sys."
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33 source="stdout"
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34 level="fatal"
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35 description="Database association broken please reupload file"/>
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36 </stdio>
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37
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38 <tests>
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39 <test>
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40 <param name="input" value="fa_gc_content_input.fa"/>
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41 <output name="out_file1" file="fa_gc_content_output.txt"/>
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42 </test>
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43 </tests>
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44 <help>
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45 **Running ProHits DotPlot**
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46
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47 This runs the biclustering version of the DotPlot tool found at http://prohitstools.mshri.on.ca/. A more interactive version can be found at http://prohits-viz.lunenfeld.ca/. This script will take a long time to run.
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48
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49 INPUTS:
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50
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51 Saint Output: SAINTexpress generated "list.txt" file.
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52
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53 Primary False Discovery Rate
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54
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55 Secondary False Discovery Rate
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56
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57 Maximum Spectral Count
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58
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59 ------
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60
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61 **Please cite**
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62
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63 * Knight, J.D., Liu, G., Zhang, J., Pasculescu, A., Choi, H., and Gingras, A.-C. (2014) A web-tool for visualizing quantitative protein-protein interaction data. Proteomics, in press. PMID:25422071.
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64
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65 </help>
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66 </tool> |
