comparison SAINT_preprocessing.xml @ 63:1972ccdbeb16 draft

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62:81db20bfc349

          ${ba.assign}
          ${ba.T_C}
        #end for
        "
      \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in $Inter_file $Prey_file
    #end if
  </command>
  <requirements>
    <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
  </requirements>

    <conditional name="type_select">
      <param type="select" name="type" label="Data Source">
        <option value="MaxQuant">MaxQuant</option>
        <option value="Scaffold">Scaffold</option>
        <option value="Peptideshaker">Peptideshaker</option> 
      </param>
      <when value="MaxQuant">
        <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"/>

          <option value="Peptides">#Peptides</option>
          <option value="Unique">#Unique</option> 
          <option value="Validated_PSMs">#Validated PSMs</option>
          <option value="PSMs">#PSMs</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>

63:1972ccdbeb16

          ${ba.assign}
          ${ba.T_C}
        #end for
        "
      \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in $Inter_file $Prey_file
    #elif (str($type_select.type) == 'mzIdentML'):
      Protein_report_processing.py "$type_select.input" $type_select.bait_file_in $type_select.preybool $type_select.fasta_db \$INSTALL_RUN_PATH/ 
        "
        #for $ba in $bait
          ${ba.bait1}
          ${ba.assign}
          ${ba.T_C}
        #end for
        "
      $type_select.bait_bool $Prey_file $Bait_file $Inter_file 
    #end if
  </command>
  <requirements>
    <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
  </requirements>

    <conditional name="type_select">
      <param type="select" name="type" label="Data Source">
        <option value="MaxQuant">MaxQuant</option>
        <option value="Scaffold">Scaffold</option>
        <option value="Peptideshaker">Peptideshaker</option> 
        <option value="mzIdentML">mzIdentML</option> 
      </param>
      <when value="MaxQuant">
        <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"/>

          <option value="Peptides">#Peptides</option>
          <option value="Unique">#Unique</option> 
          <option value="Validated_PSMs">#Validated PSMs</option>
          <option value="PSMs">#PSMs</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>
      <when value="mzIdentML">
        <param format="dat" name="input" type="data" label="mzIdentML Files" multiple="true"/>
        <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>