view OpenSwathChromatogramExtractor.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

<?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: [Targeted Experiments]-->
  <tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="2.0.0">
    <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 $param_extraction_function:
  -extraction_function
  #if &quot; &quot; in str($param_extraction_function):
    &quot;$param_extraction_function&quot;
  #else
    $param_extraction_function
  #end if
#end if
-threads \${GALAXY_SLOTS:-24}
#if $param_model_type:
  -model:type
  #if &quot; &quot; in str($param_model_type):
    &quot;$param_model_type&quot;
  #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 format="mzml" help="(-in) " label="Input files separated by blank" multiple="true" name="param_in" optional="False" size="30" type="data">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param format="tabular,traml" help="(-tr) " label="transition file ('TraML' or 'csv')" name="param_tr" optional="False" type="data"/>
      <param format="trafoxml" help="(-rt_norm) " label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" name="param_rt_norm" optional="True" type="data"/>
      <param help="(-min_upper_edge_dist) " label="Minimal distance to the edge to still consider a precursor, in Thomson" name="param_min_upper_edge_dist" type="float" value="0.0"/>
      <param help="(-mz_window) e.g. 100 ppm would extract 50 ppm on either side" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag). This is the full window size," min="0.0" name="param_mz_window" optional="True" type="float" value="0.05"/>
      <param help="(-rt_window) e.g. a value of 1000 seconds would extract 500 seconds on either side" label="Extraction window in RT dimension (-1 means extract over the whole range). This is the full window size," name="param_rt_window" type="float" value="-1.0"/>
      <param checked="false" falsevalue="" help="(-is_swath) " label="Set this flag if the data is SWATH data" name="param_is_swath" optional="True" truevalue="-is_swath" type="boolean"/>
      <param checked="false" falsevalue="" help="(-ppm) " label="m/z extraction_window is in ppm" name="param_ppm" optional="True" truevalue="-ppm" type="boolean"/>
      <param checked="false" falsevalue="" help="(-extract_MS1) " label="Extract the MS1 transitions based on the precursor values in the TraML file" name="param_extract_MS1" optional="True" truevalue="-extract_MS1" type="boolean"/>
      <param help="(-extraction_function) " label="Function used to extract the signal" name="param_extraction_function" optional="True" type="select" value="tophat">
        <option value="tophat">tophat</option>
        <option value="bartlett">bartlett</option>
      </param>
      <param help="(-type) " label="Type of model" name="param_model_type" optional="True" type="select" value="linear">
        <option value="linear">linear</option>
        <option value="b_spline">b_spline</option>
        <option value="interpolated">interpolated</option>
      </param>
      <param checked="false" falsevalue="" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" name="param_model_symmetric_regression" optional="True" truevalue="-model:symmetric_regression" type="boolean"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="mzml" name="param_out"/>
    </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>