comparison TOFCalibration.xml @ 13:9f0e189d093c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

12:cfd9c633de6b

<?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: [Signal processing and preprocessing]-->
<tool id="TOFCalibration" name="TOFCalibration" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>Applies time of flight calibration.</description>
  <macros>
    <token name="@EXECUTABLE@">TOFCalibration</token>
    <import>macros.xml</import>
    <import>macros_autotest.xml</import>
    <import>macros_test.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@

  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input peak or raw data file" help=" select mzml data sets(s)"/>
    <param name="ext_calibrants" argument="-ext_calibrants" type="data" format="mzml" optional="false" label="input file containing the external calibrant spectra (peak or raw data)" help=" select mzml data sets(s)"/>
    <param name="ref_masses" argument="-ref_masses" type="data" format="tabular,txt" optional="false" label="input file containing reference masses of the external calibrant spectra (one per line)" help=" select tabular,txt data sets(s)"/>
    <param name="tof_const" argument="-tof_const" type="data" format="tabular" optional="false" label="File containing TOF conversion constants" help="These can be either two or three constants. per set, depending on the conversion type. Either one set for all calibrant spectra . (tab separated), or one for each spectrum.. For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line) select tabular data sets(s)"/>
    <param name="peak_data" argument="-peak_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag, if you have peak data, not raw data (the picking parameters are accessible only from the INI file)" help=""/>
    <section name="algorithm" title="Algorithm section for peak picking" help="" expanded="false">
      <section name="PeakPicker" title="" help="" expanded="false">
        <param name="signal_to_noise" argument="-algorithm:PeakPicker:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help=""/>
        <param name="centroid_percentage" argument="-algorithm:PeakPicker:centroid_percentage" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid" help="If it is 1 the centroid position corresponds to the position of the highest intensity"/>
        <param name="peak_width" argument="-algorithm:PeakPicker:peak_width" type="float" optional="true" min="0.0" value="0.15" label="Approximate fwhm of the peaks" help=""/>

          <param name="noise_for_empty_window" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/>
        </section>
      </section>
    </section>
    <expand macro="adv_opts_macro">
      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>

    <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <expand macro="autotest_TOFCalibration"/>
    <expand macro="manutest_TOFCalibration"/>
  </tests>
  <help><![CDATA[Applies time of flight calibration.


For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_TOFCalibration.html]]></help>
  <expand macro="references"/>
</tool>

13:9f0e189d093c

<?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: [Signal processing and preprocessing]-->
<tool id="TOFCalibration" name="TOFCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Applies time of flight calibration.</description>
  <macros>
    <token name="@EXECUTABLE@">TOFCalibration</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@

  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param argument="-in" type="data" format="mzml" optional="false" label="input peak or raw data file" help=" select mzml data sets(s)"/>
    <param argument="-ext_calibrants" type="data" format="mzml" optional="false" label="input file containing the external calibrant spectra (peak or raw data)" help=" select mzml data sets(s)"/>
    <param argument="-ref_masses" type="data" format="tabular,txt" optional="false" label="input file containing reference masses of the external calibrant spectra (one per line)" help=" select tabular,txt data sets(s)"/>
    <param argument="-tof_const" type="data" format="tabular" optional="false" label="File containing TOF conversion constants" help="These can be either two or three constants. per set, depending on the conversion type. Either one set for all calibrant spectra . (tab separated), or one for each spectrum.. For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line) select tabular data sets(s)"/>
    <param argument="-peak_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag, if you have peak data, not raw data (the picking parameters are accessible only from the INI file)" help=""/>
    <section name="algorithm" title="Algorithm section for peak picking" help="" expanded="false">
      <section name="PeakPicker" title="" help="" expanded="false">
        <param name="signal_to_noise" argument="-algorithm:PeakPicker:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help=""/>
        <param name="centroid_percentage" argument="-algorithm:PeakPicker:centroid_percentage" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid" help="If it is 1 the centroid position corresponds to the position of the highest intensity"/>
        <param name="peak_width" argument="-algorithm:PeakPicker:peak_width" type="float" optional="true" min="0.0" value="0.15" label="Approximate fwhm of the peaks" help=""/>

          <param name="noise_for_empty_window" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/>
        </section>
      </section>
    </section>
    <expand macro="adv_opts_macro">
      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>

    <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests><!-- TOPP_TOFCalibration_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="TOFCalibration_1_input.mzML"/>
      <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/>
      <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
      <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
      <param name="peak_data" value="false"/>
      <section name="algorithm">
        <section name="PeakPicker">
          <param name="signal_to_noise" value="3.0"/>
          <param name="centroid_percentage" value="0.6"/>
          <param name="peak_width" value="0.15"/>
          <param name="estimate_peak_width" value="false"/>
          <param name="fwhm_lower_bound_factor" value="0.7"/>
          <param name="fwhm_upper_bound_factor" value="20.0"/>
          <section name="optimization">
            <param name="iterations" value="400"/>
            <section name="penalties">
              <param name="position" value="0.0"/>
              <param name="left_width" value="1.0"/>
              <param name="right_width" value="1.0"/>
              <param name="height" value="1.0"/>
            </section>
            <section name="2d">
              <param name="tolerance_mz" value="2.2"/>
              <param name="max_peak_distance" value="1.2"/>
            </section>
          </section>
          <section name="thresholds">
            <param name="peak_bound" value="400.0"/>
            <param name="peak_bound_ms2_level" value="10.0"/>
            <param name="correlation" value="0.0"/>
            <param name="noise_level" value="0.1"/>
            <param name="search_radius" value="3"/>
          </section>
          <section name="wavelet_transform">
            <param name="spacing" value="0.001"/>
          </section>
          <section name="deconvolution">
            <param name="deconvolution" value="false"/>
            <param name="asym_threshold" value="0.3"/>
            <param name="left_width" value="2.0"/>
            <param name="right_width" value="2.0"/>
            <param name="scaling" value="0.12"/>
            <section name="fitting">
              <param name="fwhm_threshold" value="0.7"/>
              <param name="eps_abs" value="9.999999747378752e-06"/>
              <param name="eps_rel" value="9.999999747378752e-06"/>
              <param name="max_iteration" value="10"/>
              <section name="penalties">
                <param name="position" value="0.0"/>
                <param name="height" value="1.0"/>
                <param name="left_width" value="0.0"/>
                <param name="right_width" value="0.0"/>
              </section>
            </section>
          </section>
          <section name="SignalToNoiseEstimationParameter">
            <param name="max_intensity" value="-1"/>
            <param name="auto_max_stdev_factor" value="3.0"/>
            <param name="auto_max_percentile" value="95"/>
            <param name="auto_mode" value="0"/>
            <param name="win_len" value="200.0"/>
            <param name="bin_count" value="30"/>
            <param name="stdev_mp" value="3.0"/>
            <param name="min_required_elements" value="10"/>
            <param name="noise_for_empty_window" value="1e+20"/>
          </section>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <!-- TOPP_TOFCalibration_2 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="TOFCalibration_2_input.mzML"/>
      <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/>
      <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
      <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
      <param name="peak_data" value="true"/>
      <section name="algorithm">
        <section name="PeakPicker">
          <param name="signal_to_noise" value="3.0"/>
          <param name="centroid_percentage" value="0.6"/>
          <param name="peak_width" value="0.15"/>
          <param name="estimate_peak_width" value="false"/>
          <param name="fwhm_lower_bound_factor" value="0.7"/>
          <param name="fwhm_upper_bound_factor" value="20.0"/>
          <section name="optimization">
            <param name="iterations" value="400"/>
            <section name="penalties">
              <param name="position" value="0.0"/>
              <param name="left_width" value="1.0"/>
              <param name="right_width" value="1.0"/>
              <param name="height" value="1.0"/>
            </section>
            <section name="2d">
              <param name="tolerance_mz" value="2.2"/>
              <param name="max_peak_distance" value="1.2"/>
            </section>
          </section>
          <section name="thresholds">
            <param name="peak_bound" value="400.0"/>
            <param name="peak_bound_ms2_level" value="10.0"/>
            <param name="correlation" value="0.0"/>
            <param name="noise_level" value="0.1"/>
            <param name="search_radius" value="3"/>
          </section>
          <section name="wavelet_transform">
            <param name="spacing" value="0.001"/>
          </section>
          <section name="deconvolution">
            <param name="deconvolution" value="false"/>
            <param name="asym_threshold" value="0.3"/>
            <param name="left_width" value="2.0"/>
            <param name="right_width" value="2.0"/>
            <param name="scaling" value="0.12"/>
            <section name="fitting">
              <param name="fwhm_threshold" value="0.7"/>
              <param name="eps_abs" value="9.999999747378752e-06"/>
              <param name="eps_rel" value="9.999999747378752e-06"/>
              <param name="max_iteration" value="10"/>
              <section name="penalties">
                <param name="position" value="0.0"/>
                <param name="height" value="1.0"/>
                <param name="left_width" value="0.0"/>
                <param name="right_width" value="0.0"/>
              </section>
            </section>
          </section>
          <section name="SignalToNoiseEstimationParameter">
            <param name="max_intensity" value="-1"/>
            <param name="auto_max_stdev_factor" value="3.0"/>
            <param name="auto_max_percentile" value="95"/>
            <param name="auto_mode" value="0"/>
            <param name="win_len" value="200.0"/>
            <param name="bin_count" value="30"/>
            <param name="stdev_mp" value="3.0"/>
            <param name="min_required_elements" value="10"/>
            <param name="noise_for_empty_window" value="1e+20"/>
          </section>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Applies time of flight calibration.


For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_TOFCalibration.html]]></help>
  <expand macro="references"/>
</tool>