annotate InternalCalibration.xml @ 5:ed8100768631 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

<?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: [Signal processing and preprocessing]-->
<tool id="InternalCalibration" name="InternalCalibration" version="2.3.0">
  <description>Applies an internal mass recalibration.</description>
  <macros>
    <token name="@EXECUTABLE@">InternalCalibration</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>InternalCalibration

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_rscript_executable:
  -rscript_executable $param_rscript_executable
#end if
#if $param_ppm_match_tolerance:
  -ppm_match_tolerance $param_ppm_match_tolerance
#end if

#if $rep_param_ms_level:
-ms_level
  #for token in $rep_param_ms_level:
    #if " " in str(token):
      "$token.param_ms_level"
    #else
      $token.param_ms_level
    #end if
  #end for
#end if
#if $param_RT_chunking:
  -RT_chunking $param_RT_chunking
#end if
#if $param_cal_id_in:
  -cal:id_in $param_cal_id_in
#end if
#if $param_cal_lock_in:
  -cal:lock_in $param_cal_lock_in
#end if
#if $param_cal_lock_out:
  -cal:lock_out $param_cal_lock_out
#end if
#if $param_cal_lock_fail_out:
  -cal:lock_fail_out $param_cal_lock_fail_out
#end if
#if $param_cal_lock_require_mono:
  -cal:lock_require_mono
#end if
#if $param_cal_lock_require_iso:
  -cal:lock_require_iso
#end if
#if $param_cal_model_type:
  -cal:model_type
  #if " " in str($param_cal_model_type):
    "$param_cal_model_type"
  #else
    $param_cal_model_type
  #end if
#end if
#if $param_RANSAC_enabled:
  -RANSAC:enabled
#end if
#if $param_RANSAC_threshold:
  -RANSAC:threshold $param_RANSAC_threshold
#end if
#if $param_RANSAC_pc_inliers:
  -RANSAC:pc_inliers $param_RANSAC_pc_inliers
#end if
#if $param_RANSAC_iter:
  -RANSAC:iter $param_RANSAC_iter
#end if
#if $param_goodness_median:
  -goodness:median $param_goodness_median
#end if
#if $param_goodness_MAD:
  -goodness:MAD $param_goodness_MAD
#end if
#if $param_quality_control_models:
  -quality_control:models $param_quality_control_models
#end if
#if $param_quality_control_models_plot:
  -quality_control:models_plot $param_quality_control_models_plot
#end if
#if $param_quality_control_residuals:
  -quality_control:residuals $param_quality_control_residuals
#end if
#if $param_quality_control_residuals_plot:
  -quality_control:residuals_plot $param_quality_control_residuals_plot
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="Input peak file" help="(-in) "/>
    <param name="param_rscript_executable" type="data" format="txt" value="Rscript" label="Path to the Rscript executable (default: 'Rscript')" help="(-rscript_executable) "/>
    <param name="param_ppm_match_tolerance" type="float" value="25.0" label="Finding calibrants in raw data uses this tolerance (for lock masses and ID's)" help="(-ppm_match_tolerance) "/>
    <repeat name="rep_param_ms_level" min="0" max="1" title="param_ms_level">
      <param name="param_ms_level" type="text" size="30" value="1 2 3" label="Target MS levels to apply the transformation onto" help="(-ms_level) Does not affect calibrant collection">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_RT_chunking" type="float" value="300.0" label="RT window (one-sided, i.e" help="(-RT_chunking) left-&gt;center, or center-&gt;right) around an MS scan in which calibrants are collected to build a model. Set to -1 to use ALL calibrants for all scans, i.e. a global model"/>
    <param name="param_cal_id_in" type="data" format="idxml,featurexml" optional="True" label="Identifications or features whose peptide ID's serve as calibration masses" help="(-id_in) "/>
    <param name="param_cal_lock_in" type="data" format="tabular" optional="True" label="Input file containing reference m/z values (text file with each line as: m/z ms-level charge) which occur in all scans" help="(-lock_in) "/>
    <param name="param_cal_lock_require_mono" display="radio" type="boolean" truevalue="-cal:lock_require_mono" falsevalue="" checked="false" optional="True" label="Require all lock masses to be monoisotopic, i.e" help="(-lock_require_mono) not the iso1, iso2 etc ('charge' column is used to determine the spacing). Peaks which are not mono-isotopic are not used"/>
    <param name="param_cal_lock_require_iso" display="radio" type="boolean" truevalue="-cal:lock_require_iso" falsevalue="" checked="false" optional="True" label="Require all lock masses to have at least the +1 isotope" help="(-lock_require_iso) Peaks without isotope pattern are not used"/>
    <param name="param_cal_model_type" display="radio" type="select" optional="False" value="linear_weighted" label="Type of function to be fitted to the calibration points" help="(-model_type) ">
      <option value="linear">linear</option>
      <option value="linear_weighted" selected="true">linear_weighted</option>
      <option value="quadratic">quadratic</option>
      <option value="quadratic_weighted">quadratic_weighted</option>
    </param>
    <param name="param_RANSAC_enabled" display="radio" type="boolean" truevalue="-RANSAC:enabled" falsevalue="" checked="false" optional="True" label="Apply RANSAC to calibration points to remove outliers before fitting a model" help="(-enabled) "/>
    <param name="param_RANSAC_threshold" type="float" value="10.0" label="Threshold for accepting inliers (instrument precision (not accuracy!) as ppm^2 distance)" help="(-threshold) "/>
    <param name="param_RANSAC_pc_inliers" type="integer" min="1" max="99" optional="True" value="30" label="Minimum percentage (of available data) of inliers (&lt;threshold away from model) to accept the model" help="(-pc_inliers) "/>
    <param name="param_RANSAC_iter" type="integer" value="70" label="Maximal # iterations" help="(-iter) "/>
    <param name="param_goodness_median" type="float" value="4.0" label="The median ppm error of calibrated masses must be smaller than this threshold" help="(-median) "/>
    <param name="param_goodness_MAD" type="float" value="1.0" label="The median absolute deviation of the ppm error of calibrated masses must be smaller than this threshold" help="(-MAD) "/>
    <expand macro="advanced_options">
      <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="mzml"/>
    <data name="param_cal_lock_out" format="mzml"/>
    <data name="param_cal_lock_fail_out" format="mzml"/>
    <data name="param_quality_control_models" format="tabular"/>
    <data name="param_quality_control_models_plot" format="png"/>
    <data name="param_quality_control_residuals" format="tabular"/>
    <data name="param_quality_control_residuals_plot" format="png"/>
  </outputs>
  <help>Applies an internal mass recalibration.


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