annotate OpenSwathChromatogramExtractor.xml @ 5:ebe0e9442a29 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: [Targeted Experiments]-->
<tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="2.3.0">
  <description>Extract chromatograms (XIC) from a MS2 map file.</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathChromatogramExtractor</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>OpenSwathChromatogramExtractor

-in
  #for token in $param_in:
    $token
  #end for
#if $param_tr:
  -tr $param_tr
#end if
#if $param_rt_norm:
  -rt_norm $param_rt_norm
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_min_upper_edge_dist:
  -min_upper_edge_dist $param_min_upper_edge_dist
#end if
#if $param_mz_window:
  -mz_window $param_mz_window
#end if
#if $param_rt_window:
  -rt_window $param_rt_window
#end if
#if $param_is_swath:
  -is_swath
#end if
#if $param_ppm:
  -ppm
#end if
#if $param_extract_MS1:
  -extract_MS1
#end if
#if $param_extraction_function:
  -extraction_function
  #if " " in str($param_extraction_function):
    "$param_extraction_function"
  #else
    $param_extraction_function
  #end if
#end if
#if $param_model_type:
  -model:type
  #if " " in str($param_model_type):
    "$param_model_type"
  #else
    $param_model_type
  #end if
#end if
#if $param_model_symmetric_regression:
  -model:symmetric_regression
#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" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr) "/>
    <param name="param_rt_norm" type="data" format="trafoxml" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm) "/>
    <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help="(-min_upper_edge_dist) "/>
    <param name="param_mz_window" type="float" min="0.0" optional="True" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag). This is the full window size," help="(-mz_window) e.g. 100 ppm would extract 50 ppm on either side"/>
    <param name="param_rt_window" type="float" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range). This is the full window size," help="(-rt_window) e.g. a value of 1000 seconds would extract 500 seconds on either side"/>
    <param name="param_is_swath" display="radio" type="boolean" truevalue="-is_swath" falsevalue="" checked="false" optional="True" label="Set this flag if the data is SWATH data" help="(-is_swath) "/>
    <param name="param_ppm" display="radio" type="boolean" truevalue="-ppm" falsevalue="" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm) "/>
    <param name="param_extract_MS1" display="radio" type="boolean" truevalue="-extract_MS1" falsevalue="" checked="false" optional="True" label="Extract the MS1 transitions based on the precursor values in the TraML file" help="(-extract_MS1) "/>
    <param name="param_extraction_function" display="radio" type="select" optional="False" value="tophat" label="Function used to extract the signal" help="(-extraction_function) ">
      <option value="tophat" selected="true">tophat</option>
      <option value="bartlett">bartlett</option>
    </param>
    <param name="param_model_type" display="radio" type="select" optional="False" value="linear" label="Type of model" help="(-type) ">
      <option value="linear" selected="true">linear</option>
      <option value="b_spline">b_spline</option>
      <option value="interpolated">interpolated</option>
      <option value="lowess">lowess</option>
    </param>
    <param name="param_model_symmetric_regression" display="radio" type="boolean" truevalue="-model:symmetric_regression" falsevalue="" checked="false" optional="True" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'"/>
    <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>Extract chromatograms (XIC) from a MS2 map file.


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