annotate Bubblebeam_For_SAINT_wrapper.xml @ 29:f7b1fe03fb5b draft default tip

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<tool id="Bubblebeam_For_SAINT" name="Bubblebeam For SAINT">
  <description></description>
  <command interpreter="python">Bubblebeam_For_SAINT_wrapper.py $list_file $prey_file $crapome $color $label $cutoff $type $inc_file $exc_file $outfile $NSAF_zoom $SAINT_zoom $SAINT $NSAF \$INSTALL_RUN_PATH/</command>
  <requirements>
    <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
  </requirements>
  <inputs>
    <param type="select" name="type" label="MaxQuant or Scaffold">
      <option value="MQ">MaxQuant</option>
      <option value="SC">Scaffold</option> 
    </param>
    <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 name="color" type="select" label="Color">
        <option value="crapome">Crapome</option>
        <option value="red">Red</option>
        <option value="blue">Blue</option>
    </param>
    <param type="boolean" name="label" checked="true" label="Use Labels"/>
    <param type="float" name="cutoff" label="SAINT Score Cutoff" help="Select a value between 0 and 1 written like 0.8." value="0.8"/>
    <param format="txt" name="inc_file" type="data" label="List of Uniprot IDs to Include" optional="true"/>
    <param format="txt" name="exc_file" type="data" label="List of Uniprot IDs to Include" optional="true"/>
  </inputs>
  <outputs>
    <data format="txt" name="outfile" label="Outfile"/>    
    <data format="png" name="NSAF_zoom" label="Zoom NSAF" />
    <data format="png" name="SAINT_zoom" label="Zoom SAINT" />
    <data format="png" name="NSAF" label="NSAF" />
    <data format="png" name="SAINT" label="SAINT" />
  </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>
**Post-processing:**

Once SAINTexpress has been run, APOSTL is able to read the resulting "list.txt" file. Fromhere APOSTL does a number of things:

APOSTL calculates NSAF values for each prey based on the average spectra observed for each bait

OPTIONAL: APOSTL calculates the probability of a specific interaction based on prey revalence in the CRAPome 

Bubble graphs are generated for each bait where:

 * x axis is the natural log of the NSAF values
 * y axis is the observed log2 fold change (as compared to control)
 * bubble radius is proportional to the average observed spectra

OPTIONAL: bubble color corresponds to the CRAPome probability of a specific interaction in which an 80% cutoff is applied where prey with less than 80% are colored tan

APOSTL queries ConsensusPathDB for protein-protein interactions within your data and then formats the resulting network for simple cytoscape import using the "import network from file" option.

INPUTS:

MaxQuant or Scaffold:

Select Scaffold if using Scaffold output and MaxQunat if using pepetides.txt from MaxQuant software.

List File: 

SAINTexpress generated "list.txt" file

Prey File:

SAINT pre-processing generated "prey.txt" file used to run SAINTexpress

Crapome File:

Raw output from Crapome Workflow 1 query (http://www.crapome.org)

Color:

Specify the color of the bubbles within the graph.

If "crapome" is chosen and 'crapome' file is specified, bubbles will be color based on crapome specificity

Use labels:

Adds gene name labels to bubbles within the "zoomed in" graphs

SAINT Score Cutoff:

Choose Saintscore cutoff (between 0-1) to be used for filtering the "zoomed in" graphs (default = 0.8)

Also used for filtering during the generation of the cytoscape network

Species:

Human, mouse, or yeast

Interaction Confidence:

Interaction confidence value (0-1) used to filter the interactions with the ConsensusPathDB database

Suggestions:

 * low: 0
 * medium: 0.5
 * high: 0.7
 * very high: 0.9

List of Uniprot IDs to Include:

Text file with one column of uniprot IDs. Only the Uniprot IDs in the file will be used on the resulting bubblebeam.

List of Uniprot IDs to Exclude:

Text file with one column of uniprot IDs. The Uniprot IDs in this list will not be used in generating the bubblebeam.

OUTPUTS:

Bubble Graphs:

Unfiltered Data:

* NSAF v. Log2(FoldChange)
* SAINTscore v. Log2(FoldChange)

Filtered by SAINT Score

* NSAF v. Log2(FoldChange)
* SAINTscore v. Log2(FoldChange)  

Output.txt

SAINTexpress "list.txt" output with additional columns that were used during the analysis.
  </help>
</tool>