comparison peptide_indexer.xml @ 4:1183846e70a1 draft

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3:8fa16707e162

    <configfile name="config">[simple_options]
in=$input1
fasta=$database
out=$output
decoy_string=$decoy_string
#if $decoy_string_position == "prefix"
prefix=true
#end if
$extact_search
$write_protein_sequence
$keep_unreferenced_proteins
aaa_max=$aaa_max
</configfile>
  </configfiles>
  <inputs>
    <param name="input1" label="Identification Input" type="data" format="idxml" />
    <param name="database" label="Database" type="data" format="fasta" />
    <param name="decoy_string" type="text" value="_rev" label="Decoy string"/>
    <param name="decoy_string_position" type="select" label="Decoy Position">
      <option value="suffix" selected="true">Suffix</option>
      <option value="prefix">Prefix</option>
    </param>    
    <param name="extact_search" label="Exact Search" type="boolean" truevalue="" falsevalue="full_tolerant_search=true" checked="true" />
    <param name="write_protein_sequence" type="boolean" truevalue="write_protein_sequence=true" falsevalue="" checked="false" label="Store Protein Sequences" />
    <param name="keep_unreferenced_proteins" label="Keep Unreferenced Proteins" truevalue="keep_unreferenced_proteins=true" falsevalue="" type="boolean" />
    <param name="aaa_max" type="integer" value="4" label="Maximum Number of Ambiguous Amino Acids" help=" Maximal number of ambiguous amino acids (AAA) allowed when matching to a protein DB with AAA's. AAA's are 'B', 'Z', and 'X'" />

4:1183846e70a1

    <configfile name="config">[simple_options]
in=$input1
fasta=$database
out=$output
decoy_string=$decoy_string
prefix=$prefix
$extact_search
$write_protein_sequence
$keep_unreferenced_proteins
aaa_max=$aaa_max
</configfile>
  </configfiles>
  <inputs>
    <param name="input1" label="Identification Input" type="data" format="idxml" />
    <param name="database" label="Database" type="data" format="fasta" />
    <param name="decoy_string" type="text" value="_rev" label="Decoy string"/>
    <param name="prefix" type="select" label="Decoy Position">
      <option value="false" selected="true">Suffix</option>
      <option value="true">Prefix</option>
    </param>    
    <param name="extact_search" label="Exact Search" type="boolean" truevalue="" falsevalue="full_tolerant_search=true" checked="true" />
    <param name="write_protein_sequence" type="boolean" truevalue="write_protein_sequence=true" falsevalue="" checked="false" label="Store Protein Sequences" />
    <param name="keep_unreferenced_proteins" label="Keep Unreferenced Proteins" truevalue="keep_unreferenced_proteins=true" falsevalue="" type="boolean" />
    <param name="aaa_max" type="integer" value="4" label="Maximum Number of Ambiguous Amino Acids" help=" Maximal number of ambiguous amino acids (AAA) allowed when matching to a protein DB with AAA's. AAA's are 'B', 'Z', and 'X'" />