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1 <tool id="nsaf_scoring" name="NSAF Scoring Table">
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2 <description></description>
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3 <command interpreter="python">nsaf_scoring.py $list_file $prey_file $crapome $inter_file $outfile \$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="list_file" type="data" label="List File"/>
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9 <param format="txt" name="prey_file" type="data" label="Prey File"/>
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10 <param format="txt" name="crapome" type="data" label="Crapome File" optional="true"/>
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11 <param format="txt" name="inter_file" type="data" label="Inter File" />
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12 </inputs>
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13 <outputs>
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14 <data format="txt" name="outfile" label="NSAF Scored Table"/>
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15 </outputs>
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16 <stdio>
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17 <regex match="ValueError: 'PreyGene' is not in list"
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18 source="stdout"
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19 level="fatal"
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20 description="Error: Check Input file."/>
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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 </stdio>
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30 <tests>
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31 <test>
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32 <param name="input" value="fa_gc_content_input.fa"/>
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33 <output name="out_file1" file="fa_gc_content_output.txt"/>
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34 </test>
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35 </tests>
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36 <help>
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37 NSAF Scoring Table
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38 ^^^^^^^^^^^^^^^^^^
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39
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40 The NSAF score is the ratio of the NSAF for test preys versus control preys normalized by the number of controls.
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41 The NSAF score performs similarly to the SaintScore in spectral counting data following a sigmoidal relationship
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42 whereas with MS1 intensity data, NSAF scoring tracks sigmoidally to the log2 fold-change. The NSAF score is
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43 designed as a less stringent alternative to the SaintScore to complement the analysis, functioning as an empirical fold-change.
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44
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45 --------------
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46
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47 **1) SAINT Output File**
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48
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49 SAINTexpress generated *list.txt* file.
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50
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51 **Note:** Prey IDs must be in Uniprot/Swissprot format (e.g.
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52 "EGFR\_HUMAN" or "P00533").
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53
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54 **2) Prey File**
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55
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56 Please specify a *Prey* file for Bubble Graph creation. A *Prey* file
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57 should contain three columns: prey (protein) name, prey amino acid
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58 length, and prey gene name.
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59
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60 **3) CRAPome File**
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61
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62 Please specify an *CRAPome* file for Bubble Graph creation. An *Inter*
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63 file should contain five columns: IP name, Mapped Gene Symbol, Number of
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64 Experiments (ratio), and Average spectral counts, and Max spectral counts.
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65
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66 **4) Interactions File**
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67
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68 Please specify an *Inter* file for Bubble Graph creation. An *Inter*
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69 file should contain four columns: IP name, bait name, prey name, and
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70 spectral counts or intensity values, depending on the mode of
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71 quantification.
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72
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73 </help>
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74 </tool> |