<tool id="saint_wrapper" name="SAINTexpress">
  <description></description>
  <command interpreter="python">saint_wrapper.py $inter_input $prey_input $bait_input $rep_num $vc_bool $vc_num $go_bool $go_file $SAINT_output \$INSTALL_RUN_PATH/</command>
  <requirements>
    <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
  </requirements>
  <inputs>
    <param format="txt" name="inter_input" type="data" label="Interactions File"/>
    <param format="txt" name="prey_input" type="data" label="Prey File"/>
    <param format="txt" name="bait_input" type="data" label="Bait File"/>
    <param name="rep_num" type="integer" value="100" label="Number of Replicates" help="the number of replicates (with largest spectral counts or intensities) to be used for probability calculation in each bait.  This option is useful when some baits have more replicates than others." />
    <param type="boolean" name="vc_bool" checked="false" label="Using Virtual Control Purifications by Compression"/>
    <param name="vc_num" type="integer" value="1" label="Number of Virtual Controls" />
    <param type="boolean" name="go_bool" checked="false" label="Incorporate External Data Sources" />
    <param format="txt" name="go_file" type="data" optional="true" label="External Data File" help="SAINT can be run with the known interaction data in hand and it will incorporate the number of observed interactions into the statistics to boost identification probability."/>
  </inputs>
  <outputs>
    <data format="txt" name="SAINT_output" />
  </outputs>
  <stdio>
    <regex match="Error|error"
     source="stdout"
           level="fatal"
           description="Unknown error"/>
    <regex match="Error|error"
     source="stderr"
           level="fatal"
           description="Unknown error"/>
    <regex match="Error: bad bait"
           source="stdout"
           level="fatal"
           description="Error: bad bait"/>
  </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>
SAINTexpress
------------

This tool will read in a *Bait File, Prey File,* and *Inter File* and
analyze them using the latest version of SAINTexpress.

**1) Interactions File**

Please specify an *Inter* file for SAINTexpress analysis. 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.

**2) Prey File**

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

**3) Bait File**

Please specify a *Bait* file for SAINTexpress analysis. A *Bait* file
should have three columns: IP name, bait name, and the indicator for
test and negative control purifications.

**4) Number of Replicates**

The number of replicates (with largest spectral counts or intensities)
to be used for probability calculation in each bait. This option is
useful when some baits have more replicates than others.

**5) Using Virtual Control Purifications by Compression**

Sets the number of virtual control purifications by compression. For
instance, if you wish to take 4 largest spectral counts for controls,
set **Number of Vitual Controls** to 4 and this variable to Yes.

**6) Number of Virtual Controls**

Specify the number of virtual control purifications by compression.

**7) Incorporate External Data Sources**

To incorporate external data sources for computing the Topology-Aware
Probability Score (TopoAvgP), the user must also provide the interaction
database file that contains two columns: interaction identifier column
and interaction/grouping information column. The first column is just
for formality and thus can be filled in with anything (no white space)
and it will not be utilized in the scoring. The second column must be
formatted as a list of prey identifiers (consistent with the first
column of the prey file) separated by a white space.

**8) External Data File**

Specify external data file

--------

**Please cite** 

 * Choi, H., Larsen, B., Lin., Z.-Y., Breitkreutz, A., Mellacheruvu, D., Fermin, D., Qin, Z.S., Tyers, M., Gingras, A.-C. and Nesvizhskii, A.I. (2011) SAINT: probabilistic scoring of affinity purification - mass spectrometry data. Nature Methods, 8:70-3. 

  </help>
</tool>