annotate FeatureFinderMRM.xml @ 16:ccc041d26ee1 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

<!--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: [Quantitation]-->
<tool id="FeatureFinderMRM" name="FeatureFinderMRM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Detects two-dimensional features in LC-MS data</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureFinderMRM</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in &&
cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
mkdir out &&

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in
'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-out
'out/output.${gxy2omsext("featurexml")}'

## Postprocessing
&& mv 'out/output.${gxy2omsext("featurexml")}' '$out'
#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv '@EXECUTABLE@.ctd' '$ctd_out'
#end if]]></command>
  <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" label="input file" help=" select mzml data sets(s)"/>
    <section name="algorithm" title="Algorithm section" help="" expanded="false">
      <param name="min_rt_distance" argument="-algorithm:min_rt_distance" type="float" min="0.0" value="10.0" label="Minimal distance of MRM features in seconds" help=""/>
      <param name="min_num_peaks_per_feature" argument="-algorithm:min_num_peaks_per_feature" type="integer" min="1" value="5" label="Minimal number of peaks which are needed for a single feature" help=""/>
      <param name="min_signal_to_noise_ratio" argument="-algorithm:min_signal_to_noise_ratio" type="float" min="0.0" value="2.0" label="Minimal S/N ratio a peak must have to be taken into account" help="Set to zero if the MRM-traces contains mostly signals, and no noise"/>
      <param name="write_debug_files" argument="-algorithm:write_debug_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, for each feature a plot will be created, in the subdirectory 'debug'" help=""/>
      <param name="resample_traces" argument="-algorithm:resample_traces" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimension" help=""/>
      <param name="write_debuginfo" argument="-algorithm:write_debuginfo" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, debug messages are written, the output can be somewhat lengthy" help=""/>
    </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" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
        <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>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <!-- TOPP_FeatureFinderMRM_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="FeatureFinderMRM_1_input.mzML"/>
      <output name="out" value="FeatureFinderMRM_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
      <section name="algorithm">
        <param name="min_rt_distance" value="10.0"/>
        <param name="min_num_peaks_per_feature" value="5"/>
        <param name="min_signal_to_noise_ratio" value="2.0"/>
        <param name="write_debug_files" value="false"/>
        <param name="resample_traces" value="false"/>
        <param name="write_debuginfo" value="false"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
  </tests>
  <help><![CDATA[Detects two-dimensional features in LC-MS data.


For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderMRM.html]]></help>
  <expand macro="references"/>
</tool>