comparison SAINT_preprocessing.xml @ 61:0b4450bdc6a9 draft

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60:3c0ed536029e

<tool id="SAINT_preprocessing_v5" name="SAINT pre-processing">
  <description></description>
  <command interpreter="python">
    #if (str($type_select.type) == 'Scaffold'):
      SAINT_preprocessing.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/ $bait_bool $bait_file_in
    #elif (str($type_select.type) == 'MaxQuant'):
      SAINT_preprocessing_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/ $bait_bool $bait_file_in
    #elif (str($type_select.type) == 'Peptideshaker'):
      Protein_report_processing.py "$input" $Bait_file $use_metric $fasta_db $preybool 
        "
        #for $ba in $bait
          ${ba.bait1}
          ${ba.assign}
          ${ba.T_C}
        #end for
        "
      \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in $Inter_file $Prey_file
    #end if
  </command>
  <requirements>
    <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
  </requirements>

        <param format="dat" name="input" type="data" label="MaxQuant peptides 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" optional="true"/>
        <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
        <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
        <repeat name="bait" title="Bait Create">
          <param name="bait1" type="text" size="100" label="Bait"/>
          <param name="assign" type="text" size="100" label="Group Assignment"/>
          <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/> 
        </repeat>
      </when>
      <when value="Scaffold">
        <param format="dat" name="input" type="data" label="Scaffold 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" optional="true"/>
        <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
        <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
        <repeat name="bait" title="Bait Create">
          <param name="bait1" type="text" size="100" label="Bait"/>
          <param name="assign" type="text" size="100" label="Group Assignment"/>
          <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/> 
        </repeat>
      </when>
      <when value="Peptideshaker">
        <param format="dat" name="input" type="data" label="Peptideshaker Output" multiple="true"/>
        <param type="select" name="use_metric" label="Select Report File Value for Quantification">
          <option value="Validated_Peptides">#Validated Peptides</option>

        </param>
        <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
        <param type="data" name="fasta_db" format="fasta"  label="Provide Uniprot Fasta database" optional="true"/>
        <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
        <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
        <repeat name="bait" title="Bait Create">
          <param name="bait1" type="text" size="100" label="Bait"/>
          <param name="assign" type="text" size="100" label="Group Assignment"/>
          <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/> 
        </repeat>
      </when>
    </conditional>
  </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" />

61:0b4450bdc6a9

<tool id="SAINT_preprocessing_v5" name="SAINT pre-processing">
  <description></description>
  <command interpreter="python">
    #if (str($type_select.type) == 'Scaffold'):
      SAINT_preprocessing.py $type_select.input $type_select.preybool $type_select.fasta_db $type_select.Inter_file $type_select.Prey_file 
      "
        #for $ba in $bait
         ${ba.bait1}
         ${ba.assign}
         ${ba.T_C}
        #end for
        "
      $type_select.Bait_file \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in
    #elif (str($type_select.type) == 'MaxQuant'):
      SAINT_preprocessing_mq_pep.py $type_select.input $type_select.preybool $type_select.fasta_db $type_select.Inter_file $type_select.Prey_file 
        "
        #for $ba in $bait
          ${ba.bait1}
          ${ba.assign}
          ${ba.T_C}
        #end for
        "
      $type_select.Bait_file \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in
    #elif (str($type_select.type) == 'Peptideshaker'):
      Protein_report_processing.py "$type_select.input" $type_select.Bait_file $type_select.use_metric $type_select.fasta_db $type_select.preybool 
        "
        #for $ba in $bait
          ${ba.bait1}
          ${ba.assign}
          ${ba.T_C}
        #end for
        "
      \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in $type_select.Inter_file $type_select.Prey_file
    #end if
  </command>
  <requirements>
    <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
  </requirements>

        <param format="dat" name="input" type="data" label="MaxQuant peptides 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" optional="true"/>
        <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
        <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
      </when>
      <when value="Scaffold">
        <param format="dat" name="input" type="data" label="Scaffold 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" optional="true"/>
        <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
        <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
      </when>
      <when value="Peptideshaker">
        <param format="dat" name="input" type="data" label="Peptideshaker Output" multiple="true"/>
        <param type="select" name="use_metric" label="Select Report File Value for Quantification">
          <option value="Validated_Peptides">#Validated Peptides</option>

        </param>
        <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
        <param type="data" name="fasta_db" format="fasta"  label="Provide Uniprot Fasta database" optional="true"/>
        <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
        <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
      </when>
    </conditional>
    <repeat name="bait" title="Bait Create">
      <param name="bait1" type="text" size="100" label="Bait"/>
      <param name="assign" type="text" size="100" label="Group Assignment"/>
      <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" />