view NoiseFilterGaussian.xml @ 13:47982606f542 draft default tip

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

<?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="NoiseFilterGaussian" name="NoiseFilterGaussian" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).</description>
  <macros>
    <token name="@EXECUTABLE@">NoiseFilterGaussian</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 &&
ln -s '$in' 'in/${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("mzml")}'

## Postprocessing
&& mv 'out/output.${gxy2omsext("mzml")}' '$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" optional="false" label="input raw data file" help=" select mzml data sets(s)"/>
    <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
      <param name="gaussian_width" argument="-algorithm:gaussian_width" type="float" optional="true" value="0.2" label="Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z)" help=""/>
      <param name="ppm_tolerance" argument="-algorithm:ppm_tolerance" type="float" optional="true" value="10.0" label="Gaussian width, depending on the m/z position" help="The higher the value, the wider the peak and therefore the wider the gaussian"/>
      <param name="use_ppm_tolerance" argument="-algorithm:use_ppm_tolerance" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, instead of the gaussian_width value, the ppm_tolerance is used" help="The gaussian is calculated in each step anew, so this is much slower"/>
      <param name="write_log_messages" argument="-algorithm:write_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="true: Warn if no signal was found by the Gauss filter algorithm" help=""/>
    </section>
    <expand macro="adv_opts_macro">
      <param argument="-processOption" type="select" optional="true" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="">
        <option value="inmemory" selected="true">inmemory</option>
        <option value="lowmemory">lowmemory</option>
        <expand macro="list_string_san" name="processOption"/>
      </param>
      <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>
  </inputs>
  <outputs>
    <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_NoiseFilterGaussian_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="processOption" value="inmemory"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="NoiseFilterGaussian_1_input.mzML"/>
      <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <section name="algorithm">
        <param name="gaussian_width" value="1.0"/>
        <param name="ppm_tolerance" value="10.0"/>
        <param name="use_ppm_tolerance" value="false"/>
        <param name="write_log_messages" 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>
    </test>
    <!-- TOPP_NoiseFilterGaussian_2 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="processOption" value="inmemory"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/>
      <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <section name="algorithm">
        <param name="gaussian_width" value="50.0"/>
        <param name="ppm_tolerance" value="10.0"/>
        <param name="use_ppm_tolerance" value="false"/>
        <param name="write_log_messages" 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>
    </test>
    <!-- TOPP_NoiseFilterGaussian_3 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="processOption" value="lowmemory"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="NoiseFilterGaussian_1_input.mzML"/>
      <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <section name="algorithm">
        <param name="gaussian_width" value="1.0"/>
        <param name="ppm_tolerance" value="10.0"/>
        <param name="use_ppm_tolerance" value="false"/>
        <param name="write_log_messages" 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>
    </test>
    <!-- TOPP_NoiseFilterGaussian_4 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="processOption" value="lowmemory"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/>
      <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <section name="algorithm">
        <param name="gaussian_width" value="50.0"/>
        <param name="ppm_tolerance" value="10.0"/>
        <param name="use_ppm_tolerance" value="false"/>
        <param name="write_log_messages" 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>
    </test>
  </tests>
  <help><![CDATA[Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).


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