annotate SAINT_preprocessing_v5.xml @ 5:2b631809150b draft

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<tool id="SAINT_preprocessing_v5" name="SAINT pre-processing">
  <description></description>
  <command interpreter="python">
    #if (str($type) == 'Scaffold'):
      SAINT_preprocessing_v6.py $input $preybool $fasta_db $Inter_file $Prey_file 
      "
        #for $ba in $bait
         ${ba.bait1}
         ${ba.assign}
         ${ba.T_C}
        #end for
        "
      $Bait_file \$INSTALL_RUN_PATH/
    #elif (str($type) == 'MaxQuant'):
      SAINT_preprocessing_v6_mq_pep.py $input $preybool $fasta_db $Inter_file $Prey_file 
        "
        #for $ba in $bait
          ${ba.bait1}
          ${ba.assign}
          ${ba.T_C}
        #end for
        "
      $Bait_file \$INSTALL_RUN_PATH/
    #end if
  </command>
  <requirements>
    <requirement type="set_environment">INSTALL_RUN_PATH</requirment>
  </requirments>
  <inputs>
    <param type="select" name="type" label="MaxQuant or Scaffold">
      <option value="MaxQuant">MaxQuant</option>
      <option value="Scaffold">Scaffold</option> 
    </param>
    <param format="dat" name="input" type="data" label="Scaffold or MaxQuant proteinGroup Output"/>
    <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
    <param type="data" name="fasta_db" format="fasta"  label="Provide Uniprot Fasta database" />
    <repeat name="bait" title="Bait Create">
      <param name="bait1" type="text" size="100"/>
      <param name="assign" type="text" size="100"/>
      <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/>
    </repeat>
  </inputs>
  <outputs>
    <data format="txt" name="Inter_file" label="Inter File"/>    
    <data format="txt" name="Prey_file" label="Prey File" />
    <data format="txt" name="Bait_file" label="Bait File" />
  </outputs>
  <stdio>
    <regex match="error"
	   source="stdout"
           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>
Pre-processing:
APOSTL is able to recognize either a Scaffold "Samples Report" file (tab-delimited
txt file) or the "peptides.txt" file output in the maxquant "txt" output folder. No
modifications should be made to these files. Using the "Bait Create" tool, you can
create your "bait.txt" file. It is important that the individual bait names match the
bait names within your scaffold or maxquant output. APOSTL uses the bait file to find
the user's baits of interest. Additionally there is an option to make the prey file (Y/N).
When making a prey file, APOSTL queries uniprot in order to extract protein amino acid
lengths and gene names. This takes several minutes depending on your internet connection. 
Some users may want to run SAINTexpress using the same data set while changing which baits 
are considered test or control. It is useful to toggle "Make Prey" off in order to save 
time by circumventing this step as the same prey file can be used for both SAINTexpress 
runs. 

INPUTS:

Scaffold file:

- Scaffold "Samples Report" output (tab-delimited txt file)


Maxquant file:

- maxquant "peptides.txt" file (tab-delimited txt file)
  </help>
</tool>