comparison MetaboliteSpectralMatcher.xml @ 9:7b5df538705e draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"

8:da8c663a5564

<?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: [Utilities]-->
<tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="2.3.0">
  <description>Perform a spectral library search.</description>
  <macros>
    <token name="@EXECUTABLE@">MetaboliteSpectralMatcher</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[MetaboliteSpectralMatcher

#if $param_in:
  -in $param_in
#end if
#if $param_database:
  -database $param_database
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_algorithm_prec_mass_error_value:
  -algorithm:prec_mass_error_value $param_algorithm_prec_mass_error_value
#end if
#if $param_algorithm_frag_mass_error_value:
  -algorithm:frag_mass_error_value $param_algorithm_frag_mass_error_value
#end if
#if $param_algorithm_mass_error_unit:
  -algorithm:mass_error_unit
  #if " " in str($param_algorithm_mass_error_unit):
    "$param_algorithm_mass_error_unit"
  #else
    $param_algorithm_mass_error_unit
  #end if
#end if
#if $param_algorithm_report_mode:
  -algorithm:report_mode
  #if " " in str($param_algorithm_report_mode):
    "$param_algorithm_report_mode"
  #else
    $param_algorithm_report_mode
  #end if
#end if
#if $param_algorithm_ionization_mode:
  -algorithm:ionization_mode
  #if " " in str($param_algorithm_ionization_mode):
    "$param_algorithm_ionization_mode"
  #else
    $param_algorithm_ionization_mode
  #end if
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
]]></command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="Input spectra" help="(-in) "/>
    <param name="param_database" type="data" format="mzml" optional="True" value="CHEMISTRY/MetaboliteSpectralDB.mzML" label="Default spectral database" help="(-database) "/>
    <param name="param_algorithm_prec_mass_error_value" type="float" value="100.0" label="Error allowed for precursor ion mass" help="(-prec_mass_error_value) "/>
    <param name="param_algorithm_frag_mass_error_value" type="float" value="500.0" label="Error allowed for product ions" help="(-frag_mass_error_value) "/>
    <param name="param_algorithm_mass_error_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of mass error (ppm or Da)" help="(-mass_error_unit) ">
      <option value="ppm" selected="true">ppm</option>
      <option value="Da">Da</option>
    </param>
    <param name="param_algorithm_report_mode" display="radio" type="select" optional="False" value="top3" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="(-report_mode) ">
      <option value="top3" selected="true">top3</option>
      <option value="best">best</option>
    </param>
    <param name="param_algorithm_ionization_mode" display="radio" type="select" optional="False" value="positive" label="Positive or negative ionization mode?" help="(-ionization_mode) ">
      <option value="positive" selected="true">positive</option>
      <option value="negative">negative</option>
    </param>
    <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) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="tabular"/>
  </outputs>
  <help>Perform a spectral library search.


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

9:7b5df538705e

<?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: [Utilities]-->
<tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>Perform a spectral library search.</description>
  <macros>
    <token name="@EXECUTABLE@">MetaboliteSpectralMatcher</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($in.ext)' &&
mkdir database &&
ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.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($in.ext)'
-database
'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)'
-out
'out/output.${gxy2omsext("mztab")}'

## Postprocessing
&& mv 'out/output.${gxy2omsext("mztab")}' '$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 spectra" help=" select mzml data sets(s)"/>
    <param name="database" argument="-database" type="data" format="mzml" optional="false" label="Default spectral database" help=" select mzml data sets(s)"/>
    <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
      <param name="prec_mass_error_value" argument="-algorithm:prec_mass_error_value" type="float" optional="true" value="100.0" label="Error allowed for precursor ion mass" help=""/>
      <param name="frag_mass_error_value" argument="-algorithm:frag_mass_error_value" type="float" optional="true" value="500.0" label="Error allowed for product ions" help=""/>
      <param name="mass_error_unit" argument="-algorithm:mass_error_unit" display="radio" type="select" optional="false" label="Unit of mass error (ppm or Da)" help="">
        <option value="ppm" selected="true">ppm</option>
        <option value="Da">Da</option>
        <expand macro="list_string_san"/>
      </param>
      <param name="report_mode" argument="-algorithm:report_mode" display="radio" type="select" optional="false" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="">
        <option value="top3" selected="true">top3</option>
        <option value="best">best</option>
        <expand macro="list_string_san"/>
      </param>
      <param name="ionization_mode" argument="-algorithm:ionization_mode" display="radio" type="select" optional="false" label="Positive or negative ionization mode?" help="">
        <option value="positive" selected="true">positive</option>
        <option value="negative">negative</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="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
    <data name="ctd_out" format="xml" label="${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_MetaboliteSpectralMatcher"/>
    <expand macro="manutest_MetaboliteSpectralMatcher"/>
  </tests>
  <help><![CDATA[Perform a spectral library search.


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