comparison SAINT_preprocessing.xml @ 79:a51c0e6d7d99 draft

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78:211fd8ae6edc

<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 $Inter_file $Prey_file 
      "

        #end for
        "
      $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" $Bait_file $type_select.use_metric $type_select.fasta_db $type_select.preybool 
        "
        #for $ba in $bait
          ${ba.bait1}
          ${ba.assign}
          ${ba.T_C}

        <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?"/>

79:a51c0e6d7d99

<tool id="SAINT_preprocessing_v6" 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 $Inter_file $Prey_file 
      "

        #end for
        "
      $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" $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 $Inter_file $Prey_file
    #elif (str($type_select.type) == 'Peptideshaker_ordered_input'):
      Protein_report_processing.py 
        #set $protein_files=[]
        #for $i1, $protein_input in enumerate($type_select.protein_inputs)
        #silent $protein_files.append(str($protein_input.protein_file))
        #end for
        #echo ','.join($protein_files)
        $Bait_file $type_select.use_metric $type_select.fasta_db $type_select.preybool 
        "
        #for $ba in $bait
          ${ba.bait1}
          ${ba.assign}
          ${ba.T_C}

        <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_ordered_input">
        <repeat name = "protein_inputs" min="1" title="Input PeptideShaker Protein Result File">
            <param format="tabular" name="protein_file" type="data" label="Peptideshaker Output" multiple="false"/>
        </repeat>
        <param type="select" name="use_metric" label="Select Report File Value for Quantification">
          <option value="Validated_Peptides">#Validated Peptides</option>
          <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?"/>