annotate ExternalCalibration.xml @ 3:5f51089db166 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

<?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: [Signal processing and preprocessing]-->
<tool id="ExternalCalibration" name="ExternalCalibration" version="2.2.0">
  <description>Applies an external mass recalibration.</description>
  <macros>
    <token name="@EXECUTABLE@">ExternalCalibration</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>ExternalCalibration

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_offset:
  -offset $param_offset
#end if
#if $param_slope:
  -slope $param_slope
#end if
#if $param_power:
  -power $param_power
#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 $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_offset" type="float" value="0.0" label="Mass offset in ppm" help="(-offset) "/>
    <param name="param_slope" type="float" value="0.0" label="Slope (dependent on m/z)" help="(-slope) "/>
    <param name="param_power" type="float" value="0.0" label="Power (dependent on m/z)" help="(-power) "/>
    <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) Scans with other levels remain unchanged">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <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"/>
  </outputs>
  <help>Applies an external mass recalibration.


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