comparison PrecursorMassCorrector.xml @ 8:315dca04e06f draft

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

7:79760732d9e3

<?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="PrecursorMassCorrector" name="PrecursorMassCorrector" version="2.3.0">
  <description>Corrects the precursor entries of MS/MS spectra, by using MS1 information.</description>
  <macros>
    <token name="@EXECUTABLE@">PrecursorMassCorrector</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[PrecursorMassCorrector

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_feature_in:
  -feature_in $param_feature_in
#end if
#if $param_precursor_mass_tolerance:
  -precursor_mass_tolerance $param_precursor_mass_tolerance
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_max_charge:
  -max_charge $adv_opts.param_max_charge
#end if
    #if $adv_opts.param_intensity_threshold:
  -intensity_threshold $adv_opts.param_intensity_threshold
#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 mzML file containing the spectra" help="(-in) "/>
    <param name="param_feature_in" type="data" format="featurexml" optional="True" label="Input featureXML file, containing features; if set, the MS/MS spectra precursor entries  &lt;br&gt;will be matched to the feature m/z values if possible" help="(-feature_in) "/>
    <param name="param_precursor_mass_tolerance" type="float" min="0.0" optional="True" value="1.5" label="Maximal deviation in Th which is acceptable to be corrected; &lt;br&gt;this value should be set to the instruments selection window" help="(-precursor_mass_tolerance) "/>
    <expand macro="advanced_options">
      <param name="param_max_charge" type="integer" value="3" label="Maximal charge that should be assumed for precursor peaks" help="(-max_charge) "/>
      <param name="param_intensity_threshold" type="float" value="-1.0" label="Intensity threshold value for isotope wavelet feature finder, please look at the documentation of the class for details" help="(-intensity_threshold) "/>
      <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>Corrects the precursor entries of MS/MS spectra, by using MS1 information.


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

8:315dca04e06f

<?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="PrecursorMassCorrector" name="PrecursorMassCorrector" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>Corrects the precursor entries of MS/MS spectra, by using MS1 information.</description>
  <macros>
    <token name="@EXECUTABLE@">PrecursorMassCorrector</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 &&
#if $feature_in:
  mkdir feature_in &&
  ln -s '$feature_in' 'feature_in/${re.sub("[^\w\-_]", "_", $feature_in.element_identifier)}.$gxy2omsext($feature_in.ext)' &&
#end if

## 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")}'
#if $feature_in:
  -feature_in
  'feature_in/${re.sub("[^\w\-_]", "_", $feature_in.element_identifier)}.$gxy2omsext($feature_in.ext)'
#end if

## 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 mzML file containing the spectra" help=" select mzml data sets(s)"/>
    <param name="feature_in" argument="-feature_in" type="data" format="featurexml" optional="true" label="Input featureXML file, containing features; if set, the MS/MS spectra precursor entries" help="will be matched to the feature m/z values if possible select featurexml data sets(s)"/>
    <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" min="0.0" value="1.5" label="Maximal deviation in Th which is acceptable to be corrected;" help="this value should be set to the instruments selection window"/>
    <expand macro="adv_opts_macro">
      <param name="max_charge" argument="-max_charge" type="integer" optional="true" value="3" label="Maximal charge that should be assumed for precursor peaks" help=""/>
      <param name="intensity_threshold" argument="-intensity_threshold" type="float" optional="true" value="-1.0" label="Intensity threshold value for isotope wavelet feature finder, please look at the documentation of the class for details" help=""/>
      <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_PrecursorMassCorrector"/>
    <expand macro="manutest_PrecursorMassCorrector"/>
  </tests>
  <help><![CDATA[Corrects the precursor entries of MS/MS spectra, by using MS1 information.


For more information, visit http://www.openms.de/documentation/TOPP_PrecursorMassCorrector.html]]></help>
  <expand macro="references"/>
</tool>