annotate IDMassAccuracy.xml @ 8:3750c20d0d50 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb

<?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: [Utilities]-->
<tool id="IDMassAccuracy" name="IDMassAccuracy" version="2.3.0">
  <description>Calculates a distribution of the mass error from given mass spectra and IDs.</description>
  <macros>
    <token name="@EXECUTABLE@">IDMassAccuracy</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>IDMassAccuracy

-in
  #for token in $param_in:
    $token
  #end for
-id_in
  #for token in $param_id_in:
    $token
  #end for
#if $param_precursor_out:
  -precursor_out $param_precursor_out
#end if

#if $rep_param_precursor_columns:
-precursor_columns
  #for token in $rep_param_precursor_columns:
    #if " " in str(token):
      "$token.param_precursor_columns"
    #else
      $token.param_precursor_columns
    #end if
  #end for
#end if
#if $param_precursor_error_ppm:
  -precursor_error_ppm
#end if
#if $param_fragment_out:
  -fragment_out $param_fragment_out
#end if

#if $rep_param_fragment_columns:
-fragment_columns
  #for token in $rep_param_fragment_columns:
    #if " " in str(token):
      "$token.param_fragment_columns"
    #else
      $token.param_fragment_columns
    #end if
  #end for
#end if
#if $param_fragment_error_ppm:
  -fragment_error_ppm
#end if
#if $param_fragment_mass_tolerance:
  -fragment_mass_tolerance $param_fragment_mass_tolerance
#end if
#if $param_separator:
  -separator     "$param_separator"
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_number_of_bins:
  -number_of_bins $adv_opts.param_number_of_bins
#end if
    #if $adv_opts.param_generate_gnuplot_scripts:
  -generate_gnuplot_scripts
#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input mzML file list, containing the spectra" help="(-in) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_id_in" type="data" format="idxml" multiple="true" optional="False" size="30" label="Input idXML file list, containing the identifications" help="(-id_in) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <repeat name="rep_param_precursor_columns" min="0" max="1" title="param_precursor_columns">
      <param name="param_precursor_columns" display="radio" type="select" optional="True" value="MassDifference" label="Columns which will be written to the output file" help="(-precursor_columns) ">
        <option value="MassDifference">MassDifference</option>
      </param>
    </repeat>
    <param name="param_precursor_error_ppm" display="radio" type="boolean" truevalue="-precursor_error_ppm" falsevalue="" checked="false" optional="True" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help="(-precursor_error_ppm) "/>
    <repeat name="rep_param_fragment_columns" min="0" max="1" title="param_fragment_columns">
      <param name="param_fragment_columns" display="radio" type="select" optional="True" value="MassDifference" label="Columns which will be written to the output file" help="(-fragment_columns) ">
        <option value="MassDifference">MassDifference</option>
      </param>
    </repeat>
    <param name="param_fragment_error_ppm" display="radio" type="boolean" truevalue="-fragment_error_ppm" falsevalue="" checked="false" optional="True" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help="(-fragment_error_ppm) "/>
    <param name="param_fragment_mass_tolerance" type="float" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help="(-fragment_mass_tolerance) "/>
    <param name="param_separator" type="text" size="30" value=" " label="character which should be used to separate the columns in the output files" help="(-separator) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <expand macro="advanced_options">
      <param name="param_number_of_bins" type="integer" min="10" optional="True" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help="(-number_of_bins) "/>
      <param name="param_generate_gnuplot_scripts" display="radio" type="boolean" truevalue="-generate_gnuplot_scripts" falsevalue="" checked="false" optional="True" label="If this option is set to true, the distributions and the fits are used to generate a gnuplot script, that can be used to generate plots" help="(-generate_gnuplot_scripts) The options 'precursor_out' and 'fragment_out' must be set to take this effect"/>
      <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_precursor_out" format="tabular"/>
    <data name="param_fragment_out" format="tabular"/>
  </outputs>
  <help>Calculates a distribution of the mass error from given mass spectra and IDs.


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