comparison IDMassAccuracy.xml @ 11:65be0674bb70 draft

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

10:fe66116dfd0b

<?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="IDMassAccuracy" name="IDMassAccuracy" version="2.3.0">
  <description>Calculates a distribution of the mass error from given mass spectra and IDs.</description>
  <macros>
    <token name="@EXECUTABLE@">IDMassAccuracy</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[IDMassAccuracy

-in
  #for token in $param_in:
    $token
  #end for
-id_in
  #for token in $param_id_in:
    $token
  #end for
#if $param_precursor_out:
  -precursor_out $param_precursor_out
#end if

#if $rep_param_precursor_columns:
-precursor_columns
  #for token in $rep_param_precursor_columns:
    #if " " in str(token):
      "$token.param_precursor_columns"
    #else
      $token.param_precursor_columns
    #end if
  #end for
#end if
#if $param_precursor_error_ppm:
  -precursor_error_ppm
#end if
#if $param_fragment_out:
  -fragment_out $param_fragment_out
#end if

#if $rep_param_fragment_columns:
-fragment_columns
  #for token in $rep_param_fragment_columns:
    #if " " in str(token):
      "$token.param_fragment_columns"
    #else
      $token.param_fragment_columns
    #end if
  #end for
#end if
#if $param_fragment_error_ppm:
  -fragment_error_ppm
#end if
#if $param_fragment_mass_tolerance:
  -fragment_mass_tolerance $param_fragment_mass_tolerance
#end if
#if $param_separator:
  -separator     "$param_separator"
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_number_of_bins:
  -number_of_bins $adv_opts.param_number_of_bins
#end if
    #if $adv_opts.param_generate_gnuplot_scripts:
  -generate_gnuplot_scripts
#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
]]></command>
  <inputs>
    <param name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input mzML file list, containing the spectra" help="(-in) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_id_in" type="data" format="idxml" multiple="true" optional="False" size="30" label="Input idXML file list, containing the identifications" help="(-id_in) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <repeat name="rep_param_precursor_columns" min="0" max="1" title="param_precursor_columns">
      <param name="param_precursor_columns" display="radio" type="select" optional="True" value="MassDifference" label="Columns which will be written to the output file" help="(-precursor_columns) ">
        <option value="MassDifference">MassDifference</option>
      </param>
    </repeat>
    <param name="param_precursor_error_ppm" display="radio" type="boolean" truevalue="-precursor_error_ppm" falsevalue="" checked="false" optional="True" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help="(-precursor_error_ppm) "/>
    <repeat name="rep_param_fragment_columns" min="0" max="1" title="param_fragment_columns">
      <param name="param_fragment_columns" display="radio" type="select" optional="True" value="MassDifference" label="Columns which will be written to the output file" help="(-fragment_columns) ">
        <option value="MassDifference">MassDifference</option>
      </param>
    </repeat>
    <param name="param_fragment_error_ppm" display="radio" type="boolean" truevalue="-fragment_error_ppm" falsevalue="" checked="false" optional="True" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help="(-fragment_error_ppm) "/>
    <param name="param_fragment_mass_tolerance" type="float" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help="(-fragment_mass_tolerance) "/>
    <param name="param_separator" type="text" size="30" value=" " label="character which should be used to separate the columns in the output files" help="(-separator) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <expand macro="advanced_options">
      <param name="param_number_of_bins" type="integer" min="10" optional="True" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help="(-number_of_bins) "/>
      <param name="param_generate_gnuplot_scripts" display="radio" type="boolean" truevalue="-generate_gnuplot_scripts" falsevalue="" checked="false" optional="True" label="If this option is set to true, the distributions and the fits are used to generate a gnuplot script, that can be used to generate plots" help="(-generate_gnuplot_scripts) The options 'precursor_out' and 'fragment_out' must be set to take this effect"/>
      <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_precursor_out" format="tabular"/>
    <data name="param_fragment_out" format="tabular"/>
  </outputs>
  <help>Calculates a distribution of the mass error from given mass spectra and IDs.


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

11:65be0674bb70

<?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="IDMassAccuracy" name="IDMassAccuracy" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>Calculates a distribution of the mass error from given mass spectra and IDs.</description>
  <macros>
    <token name="@EXECUTABLE@">IDMassAccuracy</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 &&
${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
mkdir id_in &&
${ ' '.join(["ln -s '%s' 'id_in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _]) }
#if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_precursor &&
#end if
#if "out_fragment_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_fragment &&
#end if
#if "out_precursor_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_precursor_fit &&
#end if
#if "out_fragment_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_fragment_fit &&
#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
${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
-id_in
${' '.join(["'id_in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _])}
#if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_precursor
  'out_precursor/output.${gxy2omsext("tabular")}'
#end if
#if "out_fragment_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_fragment
  'out_fragment/output.${gxy2omsext("tabular")}'
#end if
#if "out_precursor_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_precursor_fit
  'out_precursor_fit/output.${gxy2omsext("tabular")}'
#end if
#if "out_fragment_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_fragment_fit
  'out_fragment_fit/output.${gxy2omsext("tabular")}'
#end if
#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
  | tee '$stdout'
#end if

## Postprocessing
#if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_precursor/output.${gxy2omsext("tabular")}' '$out_precursor'
#end if
#if "out_fragment_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_fragment/output.${gxy2omsext("tabular")}' '$out_fragment'
#end if
#if "out_precursor_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_precursor_fit/output.${gxy2omsext("tabular")}' '$out_precursor_fit'
#end if
#if "out_fragment_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_fragment_fit/output.${gxy2omsext("tabular")}' '$out_fragment_fit'
#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" multiple="true" optional="false" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/>
    <param name="id_in" argument="-id_in" type="data" format="idxml" multiple="true" optional="false" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/>
    <param name="precursor_error_ppm" argument="-precursor_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help=""/>
    <param name="fragment_error_ppm" argument="-fragment_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help=""/>
    <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help=""/>
    <expand macro="adv_opts_macro">
      <param name="number_of_bins" argument="-number_of_bins" type="integer" optional="true" min="10" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" 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="false">
      <option value="out_precursor_FLAG">out_precursor (Enables the test mode (needed for internal use only))</option>
      <option value="out_fragment_FLAG">out_fragment (Enables the test mode (needed for internal use only))</option>
      <option value="out_precursor_fit_FLAG">out_precursor_fit (Enables the test mode (needed for internal use only))</option>
      <option value="out_fragment_fit_FLAG">out_fragment_fit (Enables the test mode (needed for internal use only))</option>
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_precursor" label="${tool.name} on ${on_string}: out_precursor" format="tabular">
      <filter>OPTIONAL_OUTPUTS is not None and "out_precursor_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="out_fragment" label="${tool.name} on ${on_string}: out_fragment" format="tabular">
      <filter>OPTIONAL_OUTPUTS is not None and "out_fragment_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="out_precursor_fit" label="${tool.name} on ${on_string}: out_precursor_fit" format="tabular">
      <filter>OPTIONAL_OUTPUTS is not None and "out_precursor_fit_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="out_fragment_fit" label="${tool.name} on ${on_string}: out_fragment_fit" format="tabular">
      <filter>OPTIONAL_OUTPUTS is not None and "out_fragment_fit_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
      <filter>OPTIONAL_OUTPUTS is None</filter>
    </data>
    <data name="ctd_out" format="xml" label="${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_IDMassAccuracy"/>
    <expand macro="manutest_IDMassAccuracy"/>
  </tests>
  <help><![CDATA[Calculates a distribution of the mass error from given mass spectra and IDs.


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