comparison HighResPrecursorMassCorrector.xml @ 11:8962ca0b2456 draft

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

10:d413dc49d650

<?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="HighResPrecursorMassCorrector" name="HighResPrecursorMassCorrector" version="2.3.0">
  <description>Corrects the precursor mass and charge determined by the instrument software.</description>
  <macros>
    <token name="@EXECUTABLE@">HighResPrecursorMassCorrector</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[HighResPrecursorMassCorrector

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_out_csv:
  -out_csv $param_out_csv
#end if
#if $param_feature_in:
  -feature:in $param_feature_in
#end if
#if $param_feature_mz_tolerance:
  -feature:mz_tolerance $param_feature_mz_tolerance
#end if
#if $param_feature_mz_tolerance_unit:
  -feature:mz_tolerance_unit
  #if " " in str($param_feature_mz_tolerance_unit):
    "$param_feature_mz_tolerance_unit"
  #else
    $param_feature_mz_tolerance_unit
  #end if
#end if
#if $param_feature_rt_tolerance:
  -feature:rt_tolerance $param_feature_rt_tolerance
#end if
#if $param_feature_believe_charge:
  -feature:believe_charge
#end if
#if $param_feature_keep_original:
  -feature:keep_original
#end if
#if $param_feature_assign_all_matching:
  -feature:assign_all_matching
#end if
#if $param_nearest_peak_mz_tolerance:
  -nearest_peak:mz_tolerance $param_nearest_peak_mz_tolerance
#end if
#if $param_nearest_peak_mz_tolerance_unit:
  -nearest_peak:mz_tolerance_unit
  #if " " in str($param_nearest_peak_mz_tolerance_unit):
    "$param_nearest_peak_mz_tolerance_unit"
  #else
    $param_nearest_peak_mz_tolerance_unit
  #end if
#end if
#if $param_highest_intensity_peak_mz_tolerance:
  -highest_intensity_peak:mz_tolerance $param_highest_intensity_peak_mz_tolerance
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_feature_max_trace:
  -feature:max_trace $adv_opts.param_feature_max_trace
#end if
#end if
]]></command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="Input file (centroided data)" help="(-in) "/>
    <param name="param_feature_in" type="data" format="featurexml" optional="True" label="Features used to correct precursor masses" help="(-in) "/>
    <param name="param_feature_mz_tolerance" type="float" value="5.0" label="The precursor mass tolerance" help="(-mz_tolerance) Used to determine matching to feature mass traces"/>
    <param name="param_feature_mz_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of precursor mass tolerance" help="(-mz_tolerance_unit) ">
      <option value="Da">Da</option>
      <option value="ppm" selected="true">ppm</option>
    </param>
    <param name="param_feature_rt_tolerance" type="float" value="0.0" label="Additional retention time tolerance added to feature boundaries" help="(-rt_tolerance) "/>
    <param name="param_feature_believe_charge" display="radio" type="boolean" truevalue="-feature:believe_charge" falsevalue="" checked="false" optional="True" label="Assume precursor charge to be correct" help="(-believe_charge) "/>
    <param name="param_feature_keep_original" display="radio" type="boolean" truevalue="-feature:keep_original" falsevalue="" checked="false" optional="True" label="Make a copy of the precursor and MS2 (true) or discard the original (false)" help="(-keep_original) "/>
    <param name="param_feature_assign_all_matching" display="radio" type="boolean" truevalue="-feature:assign_all_matching" falsevalue="" checked="false" optional="True" label="Correct a precursor using all matching features (true) or only the nearest (false)" help="(-assign_all_matching) Only evaluated if copies are created (feature:keep_original)"/>
    <param name="param_nearest_peak_mz_tolerance" type="float" value="0.0" label="The precursor mass tolerance to find the closest MS1 peak" help="(-mz_tolerance) (Disable method by setting value to 0.0)"/>
    <param name="param_nearest_peak_mz_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of precursor mass tolerance" help="(-mz_tolerance_unit) ">
      <option value="Da">Da</option>
      <option value="ppm" selected="true">ppm</option>
    </param>
    <param name="param_highest_intensity_peak_mz_tolerance" type="float" value="0.0" label="The precursor mass tolerance to find the highest intensity MS1 peak (Da)" help="(-mz_tolerance) Suggested value 1/max. expected charge. (Disable method by setting value to 0.0)"/>
    <expand macro="advanced_options">
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
      <param name="param_feature_max_trace" type="integer" value="2" label="Maximum isotopic trace considered in matching a precursor to a feature" help="(-max_trace) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="mzml"/>
    <data name="param_out_csv" format="tabular"/>
  </outputs>
  <help>Corrects the precursor mass and charge determined by the instrument software.


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

11:8962ca0b2456

<?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="HighResPrecursorMassCorrector" name="HighResPrecursorMassCorrector" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>Corrects the precursor mass and charge determined by the instrument software.</description>
  <macros>
    <token name="@EXECUTABLE@">HighResPrecursorMassCorrector</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($in.ext)' &&
mkdir out &&
#if "out_csv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_csv &&
#end if
#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 "out_csv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_csv
  'out_csv/output.${gxy2omsext("csv")}'
#end if
#if $feature.in:
  -feature:in
  'feature.in/${re.sub("[^\w\-_]", "_", $feature.in.element_identifier)}.$gxy2omsext($feature.in.ext)'
#end if
#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
  | tee '$stdout'
#end if

## Postprocessing
&& mv 'out/output.${gxy2omsext("mzml")}' '$out'
#if "out_csv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_csv/output.${gxy2omsext("csv")}' '$out_csv'
#end if
#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 file (centroided data)" help=" select mzml data sets(s)"/>
    <section name="feature" title="Use features for precursor mass correction" help="" expanded="false">
      <param name="in" argument="-feature:in" type="data" format="featurexml" optional="true" label="Features used to correct precursor masses" help=" select featurexml data sets(s)"/>
      <param name="mz_tolerance" argument="-feature:mz_tolerance" type="float" optional="true" value="5.0" label="The precursor mass tolerance" help="Used to determine matching to feature mass traces"/>
      <param name="mz_tolerance_unit" argument="-feature:mz_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
        <option value="Da">Da</option>
        <option value="ppm" selected="true">ppm</option>
        <expand macro="list_string_san"/>
      </param>
      <param name="rt_tolerance" argument="-feature:rt_tolerance" type="float" optional="true" value="0.0" label="Additional retention time tolerance added to feature boundaries" help=""/>
      <param name="max_trace" argument="-feature:max_trace" type="integer" optional="true" value="2" label="Maximum isotopic trace considered in matching a precursor to a feature" help=""/>
      <param name="believe_charge" argument="-feature:believe_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assume precursor charge to be correct" help=""/>
      <param name="keep_original" argument="-feature:keep_original" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Make a copy of the precursor and MS2 (true) or discard the original (false)" help=""/>
      <param name="assign_all_matching" argument="-feature:assign_all_matching" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Correct a precursor using all matching features (true) or only the nearest (false)" help="Only evaluated if copies are created (feature:keep_original)"/>
    </section>
    <section name="nearest_peak" title="Use nearest centroided MS1 peak for precursor mass correction" help="" expanded="false">
      <param name="mz_tolerance" argument="-nearest_peak:mz_tolerance" type="float" optional="true" value="0.0" label="The precursor mass tolerance to find the closest MS1 peak" help="(Disable method by setting value to 0.0)"/>
      <param name="mz_tolerance_unit" argument="-nearest_peak:mz_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
        <option value="Da">Da</option>
        <option value="ppm" selected="true">ppm</option>
        <expand macro="list_string_san"/>
      </param>
    </section>
    <section name="highest_intensity_peak" title="Use centroided MS1 peak with the highest intensity in a certrain mass range - for precursor mass correction" help="" expanded="false">
      <param name="mz_tolerance" argument="-highest_intensity_peak:mz_tolerance" type="float" optional="true" value="0.0" label="The precursor mass tolerance to find the highest intensity MS1 peak" help="Suggested value 1/max. expected charge. (Disable method by setting value to 0.0)"/>
      <param name="mz_tolerance_unit" argument="-highest_intensity_peak:mz_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
        <option value="Da">Da</option>
        <option value="ppm" selected="true">ppm</option>
        <expand macro="list_string_san"/>
      </param>
    </section>
    <expand macro="adv_opts_macro">
      <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="out_csv_FLAG">out_csv (Unit of precursor mass tolerance)</option>
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
    <data name="out_csv" label="${tool.name} on ${on_string}: out_csv" format="csv">
      <filter>OPTIONAL_OUTPUTS is not None and "out_csv_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="ctd_out" format="xml" label="${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_HighResPrecursorMassCorrector"/>
    <expand macro="manutest_HighResPrecursorMassCorrector"/>
  </tests>
  <help><![CDATA[Corrects the precursor mass and charge determined by the instrument software.


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