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<?xml version='1.0' encoding='UTF-8'?>
<tool id="PILISIdentification" name="PILISIdentification" version="1.12.0">
  <description>performs a peptide/protein identification with the PILIS engine</description>
  <macros>
    <token name="@EXECUTABLE@">PILISIdentification</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>PILISIdentification

-in ${param_in}
-out ${param_out}
-model_file ${param_model_file}
-peptide_db_file ${param_peptide_db_file}
-precursor_mass_tolerance ${param_precursor_mass_tolerance}
-peak_mass_tolerance ${param_peak_mass_tolerance}
-max_pre_candidates ${param_max_pre_candidates}
-max_candidates ${param_max_candidates}
-upper_mz ${param_upper_mz}
-lower_mz ${param_lower_mz}
-fixed_modifications ${param_fixed_modifications}
-threads \${GALAXY_SLOTS:-24} 
-model:charge_directed_threshold ${param_charge_directed_threshold}
-model:charge_remote_threshold ${param_charge_remote_threshold}
-model:charge_loss_factor ${param_charge_loss_factor}
-model:min_y_ion_intensity ${param_min_y_ion_intensity}
-model:min_b_ion_intensity ${param_min_b_ion_intensity}
-model:min_a_ion_intensity ${param_min_a_ion_intensity}
-model:min_y_loss_intensity ${param_min_y_loss_intensity}
-model:min_b_loss_intensity ${param_min_b_loss_intensity}
-model:visible_model_depth ${param_visible_model_depth}
-model:model_depth ${param_model_depth}
${param_use_local_scoring}
${param_do_not_use_evalue_scoring}
-scoring:survival_function_bin_size ${param_survival_function_bin_size}
-scoring:global_linear_fitting_threshold ${param_global_linear_fitting_threshold}
-scoring:local_linear_fitting_threshold ${param_local_linear_fitting_threshold}
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML" optional="False" label="input file in MzML format" help="(-in)"/>
    <param name="param_model_file" type="data" format="data" label="the model file of the PILISModel" help="(-model_file)"/>
    <param name="param_peptide_db_file" type="data" format="data" label="a file which should contain peptides in the format#br#DFPIANGER 1019.09 1#br#where the first column is the peptide, the second the m/z#br#the third the charge. As a alternative the sequence file#br#may contain only peptide sequences each in a separate line#br#repectively" help="(-peptide_db_file)"/>
    <param name="param_precursor_mass_tolerance" type="float" value="2.0" label="the precursor mass tolerance" help="(-precursor_mass_tolerance)"/>
    <param name="param_peak_mass_tolerance" type="float" value="1.0" label="the peak mass tolerance" help="(-peak_mass_tolerance)"/>
    <param name="param_max_pre_candidates" type="integer" value="200" label="number of candidates that are used for precise scoring" help="(-max_pre_candidates)"/>
    <param name="param_max_candidates" type="integer" value="20" label="number of candidates that are reported by PILIS" help="(-max_candidates)"/>
    <param name="param_upper_mz" type="float" value="2000.0" label="upper mz interval endpoint" help="(-upper_mz)"/>
    <param name="param_lower_mz" type="float" value="200.0" label="lower mz interval endpoint" help="(-lower_mz)"/>
    <param name="param_fixed_modifications" type="text" size="20" label="monoisotopic_mass@residues e.g.: 57.021464@C" help="(-fixed_modifications)"/>
    <param name="param_charge_directed_threshold" type="float" value="0.3" label="bla" help="(-charge_directed_threshold)"/>
    <param name="param_charge_remote_threshold" type="float" value="0.2" label="bla" help="(-charge_remote_threshold)"/>
    <param name="param_charge_loss_factor" type="float" value="0.5" label="bla" help="(-charge_loss_factor)"/>
    <param name="param_min_y_ion_intensity" type="float" value="0.2" label="" help="(-min_y_ion_intensity)"/>
    <param name="param_min_b_ion_intensity" type="float" value="0.15" label="" help="(-min_b_ion_intensity)"/>
    <param name="param_min_a_ion_intensity" type="float" value="0.05" label="" help="(-min_a_ion_intensity)"/>
    <param name="param_min_y_loss_intensity" type="float" value="0.05" label="" help="(-min_y_loss_intensity)"/>
    <param name="param_min_b_loss_intensity" type="float" value="0.02" label="" help="(-min_b_loss_intensity)"/>
    <param name="param_visible_model_depth" type="integer" value="30" label="bla" help="(-visible_model_depth)"/>
    <param name="param_model_depth" type="integer" value="4" label="bla" help="(-model_depth)"/>
    <param name="param_use_local_scoring" type="boolean" truevalue="-scoring:use_local_scoring true" falsevalue="-scoring:use_local_scoring false" checked="false" optional="True" label="..." help="(-use_local_scoring)"/>
    <param name="param_do_not_use_evalue_scoring" type="boolean" truevalue="-scoring:do_not_use_evalue_scoring true" falsevalue="-scoring:do_not_use_evalue_scoring false" checked="false" optional="True" label="..." help="(-do_not_use_evalue_scoring)"/>
    <param name="param_survival_function_bin_size" type="integer" value="20" label="..." help="(-survival_function_bin_size)"/>
    <param name="param_global_linear_fitting_threshold" type="float" value="0.1" label="..." help="(-global_linear_fitting_threshold)"/>
    <param name="param_local_linear_fitting_threshold" type="float" value="0.5" label="..." help="(-local_linear_fitting_threshold)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="output file in idXML format" format="idXML"/>
  </outputs>
  <help>**What it does**

performs a peptide/protein identification with the PILIS engine


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PILISIdentification.html

@REFERENCES@
</help>
</tool>