annotate TICCalculator.xml @ 5:11fc1eb69276 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: [Utilities]-->
<tool id="TICCalculator" name="TICCalculator" version="2.3.0">
  <description>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).</description>
  <macros>
    <token name="@EXECUTABLE@">TICCalculator</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>TICCalculator

#if $param_in:
  -in $param_in
#end if
#if $param_read_method:
  -read_method
  #if " " in str($param_read_method):
    "$param_read_method"
  #else
    $param_read_method
  #end if
#end if
#if $param_loadData:
  -loadData
  #if " " in str($param_loadData):
    "$param_loadData"
  #else
    $param_loadData
  #end if
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
&gt; $param_stdout
</command>
  <inputs>
    <param name="param_in" type="data" format="mzData,mzxml,mzml,cachedMzML,dta,dta2d,mgf,featurexml,consensusxml,ms2,fid,tabular,peplist,kroenik,tabular" optional="False" label="Input file to convert" help="(-in) "/>
    <param name="param_read_method" type="select" optional="False" value="regular" label="Method to read the file" help="(-read_method) ">
      <option value="regular" selected="true">regular</option>
      <option value="indexed">indexed</option>
      <option value="indexed_parallel">indexed_parallel</option>
      <option value="streaming">streaming</option>
      <option value="cached">cached</option>
      <option value="cached_parallel">cached_parallel</option>
    </param>
    <param name="param_loadData" display="radio" type="select" optional="False" value="true" label="Whether to actually load and decode the binary data (or whether to skip decoding the binary data)" help="(-loadData) ">
      <option value="true" selected="true">true</option>
      <option value="false">false</option>
    </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_stdout" format="txt" label="Output from stdout"/>
  </outputs>
  <help>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).


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