view FeatureFinderIdentification.xml @ 4:e3d1e106b250 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5a45f473c5355720af88e32369b560867899e791

<?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 CTD2Galaxy.-->
<!--Proposed Tool Section: [Quantitation]-->
<tool id="FeatureFinderIdentification" name="FeatureFinderIdentification" version="2.2.0">
  <description>Detects features in MS1 data based on peptide identifications.</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureFinderIdentification</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FeatureFinderIdentification

#if $param_in:
  -in $param_in
#end if
#if $param_id:
  -id $param_id
#end if
#if $param_id_ext:
  -id_ext $param_id_ext
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_lib_out:
  -lib_out $param_lib_out
#end if
#if $param_chrom_out:
  -chrom_out $param_chrom_out
#end if
#if $param_candidates_out:
  -candidates_out $param_candidates_out
#end if
#if $param_extract_mz_window:
  -extract:mz_window $param_extract_mz_window
#end if
#if $param_extract_n_isotopes:
  -extract:n_isotopes $param_extract_n_isotopes
#end if
#if $param_detect_peak_width:
  -detect:peak_width $param_detect_peak_width
#end if
#if $param_detect_mapping_tolerance:
  -detect:mapping_tolerance $param_detect_mapping_tolerance
#end if
#if $param_svm_samples:
  -svm:samples $param_svm_samples
#end if
#if $param_svm_no_selection:
  -svm:no_selection
#end if
#if $param_svm_xval_out:
  -svm:xval_out $param_svm_xval_out
#end if
#if $param_svm_kernel:
  -svm:kernel
  #if " " in str($param_svm_kernel):
    "$param_svm_kernel"
  #else
    $param_svm_kernel
  #end if
#end if
#if $param_svm_xval:
  -svm:xval $param_svm_xval
#end if

#if $rep_param_svm_log2_C:
-svm:log2_C
  #for token in $rep_param_svm_log2_C:
    #if " " in str(token):
      "$token.param_svm_log2_C"
    #else
      $token.param_svm_log2_C
    #end if
  #end for
#end if

#if $rep_param_svm_log2_gamma:
-svm:log2_gamma
  #for token in $rep_param_svm_log2_gamma:
    #if " " in str(token):
      "$token.param_svm_log2_gamma"
    #else
      $token.param_svm_log2_gamma
    #end if
  #end for
#end if
#if $param_model_type:
  -model:type
  #if " " in str($param_model_type):
    "$param_model_type"
  #else
    $param_model_type
  #end if
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_candidates_in:
  -candidates_in $adv_opts.param_candidates_in
#end if
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_extract_isotope_pmin:
  -extract:isotope_pmin $adv_opts.param_extract_isotope_pmin
#end if
    #if $adv_opts.param_extract_rt_quantile:
  -extract:rt_quantile $adv_opts.param_extract_rt_quantile
#end if
    #if $adv_opts.param_extract_rt_window:
  -extract:rt_window $adv_opts.param_extract_rt_window
#end if
    #if $adv_opts.param_detect_min_peak_width:
  -detect:min_peak_width $adv_opts.param_detect_min_peak_width
#end if
    #if $adv_opts.param_detect_signal_to_noise:
  -detect:signal_to_noise $adv_opts.param_detect_signal_to_noise
#end if
    #if $adv_opts.param_svm_epsilon:
  -svm:epsilon $adv_opts.param_svm_epsilon
#end if
    #if $adv_opts.param_svm_cache_size:
  -svm:cache_size $adv_opts.param_svm_cache_size
#end if
    #if $adv_opts.param_svm_no_shrinking:
  -svm:no_shrinking
#end if
    #if $adv_opts.param_svm_predictors:
  -svm:predictors     "$adv_opts.param_svm_predictors"
#end if
    #if $adv_opts.param_svm_min_prob:
  -svm:min_prob $adv_opts.param_svm_min_prob
#end if
    #if $adv_opts.param_model_add_zeros:
  -model:add_zeros $adv_opts.param_model_add_zeros
#end if
    #if $adv_opts.param_model_unweighted_fit:
  -model:unweighted_fit
#end if
    #if $adv_opts.param_model_no_imputation:
  -model:no_imputation
#end if
    #if $adv_opts.param_model_check_min_area:
  -model:check:min_area $adv_opts.param_model_check_min_area
#end if
    #if $adv_opts.param_model_check_boundaries:
  -model:check:boundaries $adv_opts.param_model_check_boundaries
#end if
    #if $adv_opts.param_model_check_width:
  -model:check:width $adv_opts.param_model_check_width
#end if
    #if $adv_opts.param_model_check_asymmetry:
  -model:check:asymmetry $adv_opts.param_model_check_asymmetry
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="Input file: LC-MS raw data" help="(-in) "/>
    <param name="param_id" type="data" format="idxml" optional="False" label="Input file: Peptide identifications derived directly from 'in'" help="(-id) "/>
    <param name="param_id_ext" type="data" format="idxml" optional="True" label="Input file: 'External' peptide identifications (" help="(-id_ext) e.g. from aligned runs)"/>
    <param name="param_extract_mz_window" type="float" min="0.0" optional="True" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help="(-mz_window) "/>
    <param name="param_extract_n_isotopes" type="integer" min="2" optional="True" value="2" label="Number of isotopes to include in each peptide assay" help="(-n_isotopes) "/>
    <param name="param_detect_peak_width" type="float" min="0.0" optional="True" value="60.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="(-peak_width) Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/>
    <param name="param_detect_mapping_tolerance" type="float" min="0.0" optional="True" value="0.0" label="RT tolerance (plus/minus) for mapping peptide IDs to features" help="(-mapping_tolerance) Absolute value in seconds if 1 or greater, else relative to the RT span of the feature"/>
    <param name="param_svm_samples" type="integer" min="0" optional="True" value="0" label="Number of observations to use for training ('0' for all)" help="(-samples) "/>
    <param name="param_svm_no_selection" display="radio" type="boolean" truevalue="-svm:no_selection" falsevalue="" checked="false" optional="True" label="By default, roughly the same number of positive and negative observations, with the same intensity distribution, are selected for training" help="(-no_selection) This aims to reduce biases, but also reduces the amount of training data. Set this flag to skip this procedure and consider all available observations (subject to 'svm:samples')"/>
    <param name="param_svm_kernel" display="radio" type="select" optional="False" value="RBF" label="SVM kernel" help="(-kernel) ">
      <option value="RBF" selected="true">RBF</option>
      <option value="linear">linear</option>
    </param>
    <param name="param_svm_xval" type="integer" min="1" optional="True" value="5" label="Number of partitions for cross-validation (parameter optimization)" help="(-xval) "/>
    <repeat name="rep_param_svm_log2_C" min="0" max="1" title="param_svm_log2_C">
      <param name="param_svm_log2_C" type="text" size="30" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0" label="Values to try for the SVM parameter 'C' during parameter optimization" help="(-log2_C) A value 'x' is used as 'C = 2^x'">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <repeat name="rep_param_svm_log2_gamma" min="0" max="1" title="param_svm_log2_gamma">
      <param name="param_svm_log2_gamma" type="text" size="30" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0" label="Values to try for the SVM parameter 'gamma' during parameter optimization (RBF kernel only)" help="(-log2_gamma) A value 'x' is used as 'gamma = 2^x'">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_model_type" display="radio" type="select" optional="False" value="symmetric" label="Type of elution model to fit to features" help="(-type) ">
      <option value="symmetric" selected="true">symmetric</option>
      <option value="asymmetric">asymmetric</option>
      <option value="none">none</option>
    </param>
    <expand macro="advanced_options">
      <param name="param_candidates_in" type="data" format="featurexml" optional="True" label="Input file: Feature candidates from a previous run" help="(-candidates_in) If set, only feature classification and elution model fitting are carried out, if enabled. Many parameters are ignored"/>
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
      <param name="param_extract_isotope_pmin" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Minimum probability for an isotope to be included in the assay for a peptide" help="(-isotope_pmin) If set, this parameter takes precedence over 'extract:n_isotopes'"/>
      <param name="param_extract_rt_quantile" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="Quantile of the RT deviations between aligned internal and external IDs to use for scaling the RT extraction window" help="(-rt_quantile) "/>
      <param name="param_extract_rt_window" type="float" min="0.0" optional="True" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="(-rt_window) If set, this parameter takes precedence over 'extract:rt_quantile'"/>
      <param name="param_detect_min_peak_width" type="float" min="0.0" optional="True" value="0.2" label="Minimum elution peak width" help="(-min_peak_width) Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/>
      <param name="param_detect_signal_to_noise" type="float" min="0.1" optional="True" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help="(-signal_to_noise) "/>
      <param name="param_svm_epsilon" type="float" min="0.0" optional="True" value="0.001" label="Stopping criterion" help="(-epsilon) "/>
      <param name="param_svm_cache_size" type="float" min="1.0" optional="True" value="100.0" label="Size of the kernel cache (in MB)" help="(-cache_size) "/>
      <param name="param_svm_no_shrinking" display="radio" type="boolean" truevalue="-svm:no_shrinking" falsevalue="" checked="false" optional="True" label="Disable the shrinking heuristics" help="(-no_shrinking) "/>
      <param name="param_svm_predictors" type="text" size="30" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score" label="Names of OpenSWATH scores to use as predictors for the SVM (comma-separated list)" help="(-predictors) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param name="param_svm_min_prob" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Minimum probability of correctness, as predicted by the SVM, required to retain a feature candidate" help="(-min_prob) "/>
      <param name="param_model_add_zeros" type="float" min="0.0" optional="True" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="(-add_zeros) This parameter sets the weight given to these points during model fitting; '0' to disable"/>
      <param name="param_model_unweighted_fit" display="radio" type="boolean" truevalue="-model:unweighted_fit" falsevalue="" checked="false" optional="True" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help="(-unweighted_fit) "/>
      <param name="param_model_no_imputation" display="radio" type="boolean" truevalue="-model:no_imputation" falsevalue="" checked="false" optional="True" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help="(-no_imputation) "/>
      <param name="param_model_check_min_area" type="float" min="0.0" optional="True" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help="(-min_area) "/>
      <param name="param_model_check_boundaries" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help="(-boundaries) "/>
      <param name="param_model_check_width" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores; '0' to disable" help="(-width) "/>
      <param name="param_model_check_asymmetry" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable" help="(-asymmetry) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="featurexml"/>
    <data name="param_lib_out" format="traml"/>
    <data name="param_chrom_out" format="mzml"/>
    <data name="param_candidates_out" format="featurexml"/>
    <data name="param_svm_xval_out" format="tabular"/>
  </outputs>
  <help>Detects features in MS1 data based on peptide identifications.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderIdentification.html</help>
</tool>