<tool id="nsaf_scoring" name="NSAF Scoring Table">
  <description></description>
  <command interpreter="python">nsaf_scoring.py $list_file $prey_file $crapome $inter_file $outfile \$INSTALL_RUN_PATH/ </command>
  <requirements>
    <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
  </requirements>
  <inputs>
    <param format="txt" name="list_file" type="data" label="List File"/>
    <param format="txt" name="prey_file" type="data" label="Prey File"/>
    <param format="txt" name="crapome" type="data" label="Crapome File" optional="true"/>
    <param format="txt" name="inter_file" type="data" label="Inter File" />
  </inputs>
  <outputs>
    <data format="txt" name="outfile" label="NSAF Scored Table"/>    
  </outputs>
  <stdio>
    <regex match="ValueError: 'PreyGene' is not in list"
       source="stdout"
       level="fatal"
       description="Error: Check Input file."/>
    <regex match="Error|error"
     source="stdout"
           level="fatal"
           description="Unknown error"/>
    <regex match="Error|error"
     source="stderr"
           level="fatal"
           description="Unknown error"/>
  </stdio> 
  <tests>
    <test>
      <param name="input" value="fa_gc_content_input.fa"/>
      <output name="out_file1" file="fa_gc_content_output.txt"/>
    </test>
  </tests>
  <help>
NSAF Scoring Table
^^^^^^^^^^^^^^^^^^

The NSAF score is the ratio of the NSAF for test preys versus control preys normalized by the number of controls.
The NSAF score performs similarly to the SaintScore in spectral counting data following a sigmoidal relationship 
whereas with MS1 intensity data, NSAF scoring tracks sigmoidally to the log2 fold-change. The NSAF score is 
designed as a less stringent alternative to the SaintScore to complement the analysis, functioning as an empirical fold-change. 

--------------

**1) SAINT Output File**

SAINTexpress generated *list.txt* file.

    **Note:** Prey IDs must be in Uniprot/Swissprot format (e.g.
    "EGFR\_HUMAN" or "P00533").

**2) Prey File**

Please specify a *Prey* file for Bubble Graph creation. A *Prey* file
should contain three columns: prey (protein) name, prey amino acid
length, and prey gene name.

**3) CRAPome File**

Please specify an *CRAPome* file for Bubble Graph creation. An *Inter*
file should contain five columns: IP name, Mapped Gene Symbol, Number of 
Experiments (ratio), and Average spectral counts, and Max spectral counts.

**4) Interactions File**

Please specify an *Inter* file for Bubble Graph creation. An *Inter*
file should contain four columns: IP name, bait name, prey name, and
spectral counts or intensity values, depending on the mode of
quantification.

  </help>
</tool>