annotate MassCalculator.xml @ 4:d505219f3f15 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab

<?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: [Utilities]-->
<tool id="MassCalculator" name="MassCalculator" version="2.2.0">
  <description>Calculates masses and mass-to-charge ratios of peptide sequences</description>
  <macros>
    <token name="@EXECUTABLE@">MassCalculator</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>MassCalculator

#if $param_in:
  -in $param_in
#end if

#if $rep_param_in_seq:
-in_seq
  #for token in $rep_param_in_seq:
    #if " " in str(token):
      "$token.param_in_seq"
    #else
      $token.param_in_seq
    #end if
  #end for
#end if
#if $param_out:
  -out $param_out
#end if

#if $rep_param_charge:
-charge
  #for token in $rep_param_charge:
    #if " " in str(token):
      "$token.param_charge"
    #else
      $token.param_charge
    #end if
  #end for
#end if
#if $param_format:
  -format
  #if " " in str($param_format):
    "$param_format"
  #else
    $param_format
  #end if
#end if
#if $param_average_mass:
  -average_mass
#end if
#if $param_fragment_type:
  -fragment_type
  #if " " in str($param_fragment_type):
    "$param_fragment_type"
  #else
    $param_fragment_type
  #end if
#end if
#if $param_separator:
  -separator     "$param_separator"
#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="txt" optional="True" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help="(-in) "/>
    <repeat name="rep_param_in_seq" min="0" max="1" title="param_in_seq">
      <param name="param_in_seq" type="text" size="30" label="List of peptide sequences (mutually exclusive to 'in')" help="(-in_seq) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <repeat name="rep_param_charge" min="0" max="1" title="param_charge">
      <param name="param_charge" type="text" size="30" value="0" label="List of charge states; required if 'in_seq' is given" help="(-charge) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_format" display="radio" type="select" optional="False" value="list" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" help="(-format) ">
      <option value="list" selected="true">list</option>
      <option value="table">table</option>
      <option value="mass_only">mass_only</option>
      <option value="mz_only">mz_only</option>
    </param>
    <param name="param_average_mass" display="radio" type="boolean" truevalue="-average_mass" falsevalue="" checked="false" optional="True" label="Compute average (instead of monoisotopic) peptide masses" help="(-average_mass) "/>
    <param name="param_fragment_type" type="select" optional="False" value="full" label="For what type of sequence/fragment the mass should be computed" help="(-fragment_type) ">
      <option value="full" selected="true">full</option>
      <option value="internal">internal</option>
      <option value="N-terminal">N-terminal</option>
      <option value="C-terminal">C-terminal</option>
      <option value="a-ion">a-ion</option>
      <option value="b-ion">b-ion</option>
      <option value="c-ion">c-ion</option>
      <option value="x-ion">x-ion</option>
      <option value="y-ion">y-ion</option>
      <option value="z-ion">z-ion</option>
    </param>
    <param name="param_separator" type="text" size="30" label="Field separator for 'table' output format; by default, the 'tab' character is used" help="(-separator) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <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="txt"/>
  </outputs>
  <help>Calculates masses and mass-to-charge ratios of peptide sequences


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