view PrecursorIonSelector.xml @ 8:2faa1a2401c5 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5-dirty

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
<!--Proposed Tool Section: [Targeted Experiments]-->
<tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="2.3.0">
  <description>PrecursorIonSelector</description>
  <macros>
    <token name="@EXECUTABLE@">PrecursorIonSelector</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[PrecursorIonSelector

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_next_feat:
  -next_feat $param_next_feat
#end if
#if $param_ids:
  -ids $param_ids
#end if
#if $param_num_precursors:
  -num_precursors $param_num_precursors
#end if
#if $param_raw_data:
  -raw_data $param_raw_data
#end if
#if $param_load_preprocessing:
  -load_preprocessing
#end if
#if $param_store_preprocessing:
  -store_preprocessing
#end if
#if $param_simulation:
  -simulation
#end if
#if $param_sim_results:
  -sim_results     "$param_sim_results"
#end if
#if $param_db_path:
  -db_path $param_db_path
#end if
#if $param_rt_model:
  -rt_model     "$param_rt_model"
#end if
#if $param_dt_model:
  -dt_model     "$param_dt_model"
#end if

#if $rep_param_fixed_modifications:
-fixed_modifications
  #for token in $rep_param_fixed_modifications:
    #if " " in str(token):
      "$token.param_fixed_modifications"
    #else
      $token.param_fixed_modifications
    #end if
  #end for
#end if
#if $param_algorithm_type:
  -algorithm:type
  #if " " in str($param_algorithm_type):
    "$param_algorithm_type"
  #else
    $param_algorithm_type
  #end if
#end if
#if $param_algorithm_max_iteration:
  -algorithm:max_iteration $param_algorithm_max_iteration
#end if
#if $param_algorithm_rt_bin_capacity:
  -algorithm:rt_bin_capacity $param_algorithm_rt_bin_capacity
#end if
#if $param_algorithm_step_size:
  -algorithm:step_size $param_algorithm_step_size
#end if
#if $param_algorithm_peptide_min_prob:
  -algorithm:peptide_min_prob $param_algorithm_peptide_min_prob
#end if
#if $param_algorithm_sequential_spectrum_order:
  -algorithm:sequential_spectrum_order
#end if
#if $param_algorithm_MIPFormulation_thresholds_min_protein_probability:
  -algorithm:MIPFormulation:thresholds:min_protein_probability $param_algorithm_MIPFormulation_thresholds_min_protein_probability
#end if
#if $param_algorithm_MIPFormulation_thresholds_min_protein_id_probability:
  -algorithm:MIPFormulation:thresholds:min_protein_id_probability $param_algorithm_MIPFormulation_thresholds_min_protein_id_probability
#end if
#if $param_algorithm_MIPFormulation_thresholds_min_pt_weight:
  -algorithm:MIPFormulation:thresholds:min_pt_weight $param_algorithm_MIPFormulation_thresholds_min_pt_weight
#end if
#if $param_algorithm_MIPFormulation_thresholds_min_mz:
  -algorithm:MIPFormulation:thresholds:min_mz $param_algorithm_MIPFormulation_thresholds_min_mz
#end if
#if $param_algorithm_MIPFormulation_thresholds_max_mz:
  -algorithm:MIPFormulation:thresholds:max_mz $param_algorithm_MIPFormulation_thresholds_max_mz
#end if
#if $param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob:
  -algorithm:MIPFormulation:thresholds:min_pred_pep_prob $param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob
#end if
#if $param_algorithm_MIPFormulation_thresholds_min_rt_weight:
  -algorithm:MIPFormulation:thresholds:min_rt_weight $param_algorithm_MIPFormulation_thresholds_min_rt_weight
#end if
#if $param_algorithm_MIPFormulation_thresholds_use_peptide_rule:
  -algorithm:MIPFormulation:thresholds:use_peptide_rule
#end if
#if $param_algorithm_MIPFormulation_thresholds_min_peptide_ids:
  -algorithm:MIPFormulation:thresholds:min_peptide_ids $param_algorithm_MIPFormulation_thresholds_min_peptide_ids
#end if
#if $param_algorithm_MIPFormulation_thresholds_min_peptide_probability:
  -algorithm:MIPFormulation:thresholds:min_peptide_probability $param_algorithm_MIPFormulation_thresholds_min_peptide_probability
#end if
#if $param_algorithm_MIPFormulation_combined_ilp_k1:
  -algorithm:MIPFormulation:combined_ilp:k1 $param_algorithm_MIPFormulation_combined_ilp_k1
#end if
#if $param_algorithm_MIPFormulation_combined_ilp_k2:
  -algorithm:MIPFormulation:combined_ilp:k2 $param_algorithm_MIPFormulation_combined_ilp_k2
#end if
#if $param_algorithm_MIPFormulation_combined_ilp_k3:
  -algorithm:MIPFormulation:combined_ilp:k3 $param_algorithm_MIPFormulation_combined_ilp_k3
#end if
#if $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs:
  -algorithm:MIPFormulation:combined_ilp:scale_matching_probs
  #if " " in str($param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs):
    "$param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs"
  #else
    $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs
  #end if
#end if
#if $param_algorithm_MIPFormulation_feature_based_no_intensity_normalization:
  -algorithm:MIPFormulation:feature_based:no_intensity_normalization
#end if
#if $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature:
  -algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature
#end if
#if $param_algorithm_Preprocessing_precursor_mass_tolerance:
  -algorithm:Preprocessing:precursor_mass_tolerance $param_algorithm_Preprocessing_precursor_mass_tolerance
#end if
#if $param_algorithm_Preprocessing_precursor_mass_tolerance_unit:
  -algorithm:Preprocessing:precursor_mass_tolerance_unit
  #if " " in str($param_algorithm_Preprocessing_precursor_mass_tolerance_unit):
    "$param_algorithm_Preprocessing_precursor_mass_tolerance_unit"
  #else
    $param_algorithm_Preprocessing_precursor_mass_tolerance_unit
  #end if
#end if
#if $param_algorithm_Preprocessing_preprocessed_db_path:
  -algorithm:Preprocessing:preprocessed_db_path     "$param_algorithm_Preprocessing_preprocessed_db_path"
#end if
#if $param_algorithm_Preprocessing_preprocessed_db_pred_rt_path:
  -algorithm:Preprocessing:preprocessed_db_pred_rt_path     "$param_algorithm_Preprocessing_preprocessed_db_pred_rt_path"
#end if
#if $param_algorithm_Preprocessing_preprocessed_db_pred_dt_path:
  -algorithm:Preprocessing:preprocessed_db_pred_dt_path     "$param_algorithm_Preprocessing_preprocessed_db_pred_dt_path"
#end if
#if $param_algorithm_Preprocessing_max_peptides_per_run:
  -algorithm:Preprocessing:max_peptides_per_run $param_algorithm_Preprocessing_max_peptides_per_run
#end if
#if $param_algorithm_Preprocessing_missed_cleavages:
  -algorithm:Preprocessing:missed_cleavages $param_algorithm_Preprocessing_missed_cleavages
#end if
#if $param_algorithm_Preprocessing_taxonomy:
  -algorithm:Preprocessing:taxonomy     "$param_algorithm_Preprocessing_taxonomy"
#end if
#if $param_algorithm_Preprocessing_tmp_dir:
  -algorithm:Preprocessing:tmp_dir     "$param_algorithm_Preprocessing_tmp_dir"
#end if
#if $param_algorithm_Preprocessing_store_peptide_sequences:
  -algorithm:Preprocessing:store_peptide_sequences     "$param_algorithm_Preprocessing_store_peptide_sequences"
#end if
#if $param_algorithm_Preprocessing_rt_settings_min_rt:
  -algorithm:Preprocessing:rt_settings:min_rt $param_algorithm_Preprocessing_rt_settings_min_rt
#end if
#if $param_algorithm_Preprocessing_rt_settings_max_rt:
  -algorithm:Preprocessing:rt_settings:max_rt $param_algorithm_Preprocessing_rt_settings_max_rt
#end if
#if $param_algorithm_Preprocessing_rt_settings_rt_step_size:
  -algorithm:Preprocessing:rt_settings:rt_step_size $param_algorithm_Preprocessing_rt_settings_rt_step_size
#end if
#if $param_algorithm_Preprocessing_rt_settings_gauss_mean:
  -algorithm:Preprocessing:rt_settings:gauss_mean $param_algorithm_Preprocessing_rt_settings_gauss_mean
#end if
#if $param_algorithm_Preprocessing_rt_settings_gauss_sigma:
  -algorithm:Preprocessing:rt_settings:gauss_sigma $param_algorithm_Preprocessing_rt_settings_gauss_sigma
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_solver:
  -solver
  #if " " in str($adv_opts.param_solver):
    "$adv_opts.param_solver"
  #else
    $adv_opts.param_solver
  #end if
#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
]]></command>
  <inputs>
    <param name="param_in" type="data" format="featurexml" optional="False" label="Input feature map file (featureXML)" help="(-in) "/>
    <param name="param_ids" type="data" format="idxml" optional="False" label="file containing results of identification" help="(-ids) "/>
    <param name="param_num_precursors" type="integer" value="1" label="number of precursors to be selected" help="(-num_precursors) "/>
    <param name="param_raw_data" type="data" format="mzml" optional="True" label="Input profile data" help="(-raw_data) "/>
    <param name="param_load_preprocessing" display="radio" type="boolean" truevalue="-load_preprocessing" falsevalue="" checked="false" optional="True" label="The preprocessed db is loaded from file, not calculated" help="(-load_preprocessing) "/>
    <param name="param_store_preprocessing" display="radio" type="boolean" truevalue="-store_preprocessing" falsevalue="" checked="false" optional="True" label="The preprocessed db is stored" help="(-store_preprocessing) "/>
    <param name="param_simulation" display="radio" type="boolean" truevalue="-simulation" falsevalue="" checked="false" optional="True" label="Simulate the whole LC-MS/MS run" help="(-simulation) "/>
    <param name="param_sim_results" type="text" size="30" label="File containing the results of the simulation run" help="(-sim_results) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_db_path" type="data" format="fasta" optional="True" label="db file" help="(-db_path) "/>
    <param name="param_rt_model" type="text" size="30" label="SVM Model for RTPredict" help="(-rt_model) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_dt_model" type="text" size="30" label="SVM Model for PTPredict" help="(-dt_model) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <repeat name="rep_param_fixed_modifications" min="0" title="param_fixed_modifications">
      <param name="param_fixed_modifications" type="text" size="30" label="the modifications i.e. Carboxymethyl (C)" help="(-fixed_modifications) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_algorithm_type" type="select" optional="False" value="IPS" label="Strategy for precursor ion selection" help="(-type) ">
      <option value="ILP_IPS">ILP_IPS</option>
      <option value="IPS" selected="true">IPS</option>
      <option value="SPS">SPS</option>
      <option value="Upshift">Upshift</option>
      <option value="Downshift">Downshift</option>
      <option value="DEX">DEX</option>
    </param>
    <param name="param_algorithm_max_iteration" type="integer" min="1" optional="True" value="100" label="Maximal number of iterations" help="(-max_iteration) "/>
    <param name="param_algorithm_rt_bin_capacity" type="integer" min="1" optional="True" value="10" label="Maximal number of precursors per rt bin" help="(-rt_bin_capacity) "/>
    <param name="param_algorithm_step_size" type="integer" min="1" optional="True" value="1" label="Maximal number of precursors per iteration" help="(-step_size) "/>
    <param name="param_algorithm_peptide_min_prob" type="float" value="0.2" label="Minimal peptide probability" help="(-peptide_min_prob) "/>
    <param name="param_algorithm_sequential_spectrum_order" display="radio" type="boolean" truevalue="-algorithm:sequential_spectrum_order" falsevalue="" checked="false" optional="True" label="If true, precursors are selected sequentially with respect to their RT" help="(-sequential_spectrum_order) "/>
    <param name="param_algorithm_MIPFormulation_thresholds_min_protein_probability" type="float" min="0.0" max="1.0" optional="True" value="0.2" label="Minimal protein probability for a protein to be considered in the ILP" help="(-min_protein_probability) "/>
    <param name="param_algorithm_MIPFormulation_thresholds_min_protein_id_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="Minimal protein probability for a protein to be considered identified" help="(-min_protein_id_probability) "/>
    <param name="param_algorithm_MIPFormulation_thresholds_min_pt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal pt weight of a precurso" help="(-min_pt_weight) "/>
    <param name="param_algorithm_MIPFormulation_thresholds_min_mz" type="float" min="0.0" optional="True" value="500.0" label="Minimal mz to be considered in protein based LP formulation" help="(-min_mz) "/>
    <param name="param_algorithm_MIPFormulation_thresholds_max_mz" type="float" min="0.0" optional="True" value="5000.0" label="Minimal mz to be considered in protein based LP formulation" help="(-max_mz) "/>
    <param name="param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal predicted peptide probability of a precurso" help="(-min_pred_pep_prob) "/>
    <param name="param_algorithm_MIPFormulation_thresholds_min_rt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal rt weight of a precurso" help="(-min_rt_weight) "/>
    <param name="param_algorithm_MIPFormulation_thresholds_use_peptide_rule" display="radio" type="boolean" truevalue="-algorithm:MIPFormulation:thresholds:use_peptide_rule" falsevalue="" checked="false" optional="True" label="Use peptide rule instead of minimal protein id probability" help="(-use_peptide_rule) "/>
    <param name="param_algorithm_MIPFormulation_thresholds_min_peptide_ids" type="integer" min="1" optional="True" value="2" label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" help="(-min_peptide_ids) "/>
    <param name="param_algorithm_MIPFormulation_thresholds_min_peptide_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" help="(-min_peptide_probability) "/>
    <param name="param_algorithm_MIPFormulation_combined_ilp_k1" type="float" min="0.0" optional="True" value="0.2" label="combined ilp: weight for z_i" help="(-k1) "/>
    <param name="param_algorithm_MIPFormulation_combined_ilp_k2" type="float" min="0.0" optional="True" value="0.2" label="combined ilp: weight for x_j,s*int_j,s" help="(-k2) "/>
    <param name="param_algorithm_MIPFormulation_combined_ilp_k3" type="float" min="0.0" optional="True" value="0.4" label="combined ilp: weight for -x_j,s*w_j,s" help="(-k3) "/>
    <param name="param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs" display="radio" type="select" optional="False" value="true" label="flag if detectability * rt_weight shall be scaled to cover all [0,1]" help="(-scale_matching_probs) ">
      <option value="true" selected="true">true</option>
      <option value="false">false</option>
    </param>
    <param name="param_algorithm_MIPFormulation_feature_based_no_intensity_normalization" display="radio" type="boolean" truevalue="-algorithm:MIPFormulation:feature_based:no_intensity_normalization" falsevalue="" checked="false" optional="True" label="Flag indicating if intensities shall be scaled to be in [0,1]" help="(-no_intensity_normalization) This is done for each feature separately, so that the feature's maximal intensity in a spectrum is set to 1"/>
    <param name="param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature" type="integer" min="1" optional="True" value="1" label="The maximal number of precursors per feature" help="(-max_number_precursors_per_feature) "/>
    <param name="param_algorithm_Preprocessing_precursor_mass_tolerance" type="float" min="0.0" optional="True" value="10.0" label="Precursor mass tolerance which is used to query the peptide database for peptides" help="(-precursor_mass_tolerance) "/>
    <param name="param_algorithm_Preprocessing_precursor_mass_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Precursor mass tolerance unit" help="(-precursor_mass_tolerance_unit) ">
      <option value="ppm" selected="true">ppm</option>
      <option value="Da">Da</option>
    </param>
    <param name="param_algorithm_Preprocessing_preprocessed_db_path" type="text" size="30" label="Path where the preprocessed database should be stored" help="(-preprocessed_db_path) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_algorithm_Preprocessing_preprocessed_db_pred_rt_path" type="text" size="30" label="Path where the predicted rts of the preprocessed database should be stored" help="(-preprocessed_db_pred_rt_path) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_algorithm_Preprocessing_preprocessed_db_pred_dt_path" type="text" size="30" label="Path where the predicted rts of the preprocessed database should be stored" help="(-preprocessed_db_pred_dt_path) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_algorithm_Preprocessing_max_peptides_per_run" type="integer" min="1" optional="True" value="100000" label="Number of peptides for that the pt and rt are parallely predicted" help="(-max_peptides_per_run) "/>
    <param name="param_algorithm_Preprocessing_missed_cleavages" type="integer" min="0" optional="True" value="1" label="Number of allowed missed cleavages" help="(-missed_cleavages) "/>
    <param name="param_algorithm_Preprocessing_taxonomy" type="text" size="30" label="Taxonomy" help="(-taxonomy) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_algorithm_Preprocessing_tmp_dir" type="text" size="30" label="Absolute path to tmp data directory used to store files needed for rt and dt prediction" help="(-tmp_dir) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_algorithm_Preprocessing_store_peptide_sequences" type="text" size="30" value="false" label="Flag if peptide sequences should be stored" help="(-store_peptide_sequences) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_algorithm_Preprocessing_rt_settings_min_rt" type="float" min="1.0" optional="True" value="960.0" label="Minimal RT in the experiment (in seconds)" help="(-min_rt) "/>
    <param name="param_algorithm_Preprocessing_rt_settings_max_rt" type="float" value="3840.0" label="Maximal RT in the experiment (in seconds)" help="(-max_rt) "/>
    <param name="param_algorithm_Preprocessing_rt_settings_rt_step_size" type="float" value="30.0" label="Time between two consecutive spectra (in seconds)" help="(-rt_step_size) "/>
    <param name="param_algorithm_Preprocessing_rt_settings_gauss_mean" type="float" value="-1.0" label="mean of the gauss curve" help="(-gauss_mean) "/>
    <param name="param_algorithm_Preprocessing_rt_settings_gauss_sigma" type="float" value="3.0" label="std of the gauss curve" help="(-gauss_sigma) "/>
    <expand macro="advanced_options">
      <param name="param_solver" display="radio" type="select" optional="False" value="GLPK" label="LP solver type" help="(-solver) ">
        <option value="GLPK" selected="true">GLPK</option>
        <option value="COINOR">COINOR</option>
      </param>
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="featurexml"/>
    <data name="param_next_feat" format="featurexml"/>
  </outputs>
  <help>PrecursorIonSelector


For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PrecursorIonSelector.html</help>
</tool>