comparison NoiseFilterGaussian.xml @ 9:4b6ea1de6dc4 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"

8:26f04cb8795b

<?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="2.3.0">
  <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="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[NoiseFilterGaussian

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_algorithm_gaussian_width:
  -algorithm:gaussian_width $param_algorithm_gaussian_width
#end if
#if $param_algorithm_ppm_tolerance:
  -algorithm:ppm_tolerance $param_algorithm_ppm_tolerance
#end if
#if $param_algorithm_use_ppm_tolerance:
  -algorithm:use_ppm_tolerance
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_processOption:
  -processOption
  #if " " in str($adv_opts.param_processOption):
    "$adv_opts.param_processOption"
  #else
    $adv_opts.param_processOption
  #end if
#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
]]></command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="input raw data file" help="(-in) "/>
    <param name="param_algorithm_gaussian_width" type="float" value="0.2" label="Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z)" help="(-gaussian_width) "/>
    <param name="param_algorithm_ppm_tolerance" type="float" value="10.0" label="Gaussian width, depending on the m/z position" help="(-ppm_tolerance) &lt;br&gt;The higher the value, the wider the peak and therefore the wider the gaussian"/>
    <param name="param_algorithm_use_ppm_tolerance" display="radio" type="boolean" truevalue="-algorithm:use_ppm_tolerance" falsevalue="" checked="false" optional="True" label="If true, instead of the gaussian_width value, the ppm_tolerance is used" help="(-use_ppm_tolerance) The gaussian is calculated in each step anew, so this is much slower"/>
    <expand macro="advanced_options">
      <param name="param_processOption" display="radio" type="select" optional="False" value="inmemory" 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="(-processOption) ">
        <option value="inmemory" selected="true">inmemory</option>
        <option value="lowmemory">lowmemory</option>
      </param>
      <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>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).


For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_NoiseFilterGaussian.html</help>
</tool>

9:4b6ea1de6dc4

<?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@GALAXY_VERSION@" profile="20.05">
  <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>
    <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@
#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 name="in" 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"/>
    </section>
    <expand macro="adv_opts_macro">
      <param name="processOption" argument="-processOption" display="radio" type="select" optional="false" 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"/>
      </param>
      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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" multiple="true" label="Optional outputs" optional="true">
      <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>
    <expand macro="autotest_NoiseFilterGaussian"/>
    <expand macro="manutest_NoiseFilterGaussian"/>
  </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/documentation/TOPP_NoiseFilterGaussian.html]]></help>
  <expand macro="references"/>
</tool>