annotate ERPairFinder.xml @ 15:d6ef464ff66b draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

<?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="ERPairFinder" name="ERPairFinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description>
  <macros>
    <token name="@EXECUTABLE@">ERPairFinder</token>
    <import>macros.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($in.ext)' &&
mkdir pair_in &&
ln -s '$pair_in' 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)' &&
mkdir out &&
#if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir feature_out &&
#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($in.ext)'
-pair_in
'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)'
-out
'out/output.${gxy2omsext("consensusxml")}'
#if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -feature_out
  'feature_out/output.${gxy2omsext("featurexml")}'
#end if
#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
  | tee '$stdout'
#end if

## Postprocessing
&& mv 'out/output.${gxy2omsext("consensusxml")}' '$out'
#if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'feature_out/output.${gxy2omsext("featurexml")}' '$feature_out'
#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 argument="-in" type="data" format="mzml" optional="false" label="Input mzML file containing the ER spectra" help=" select mzml data sets(s)"/>
    <param argument="-pair_in" type="data" format="txt" optional="false" label="Pair-file in the format: m/z-light m/z-heavy charge rt" help=" select txt data sets(s)"/>
    <param argument="-precursor_mass_tolerance" type="float" optional="true" min="0.0" value="0.3" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" help=""/>
    <expand macro="adv_opts_macro">
      <param argument="-RT_tolerance" type="float" optional="true" min="1.0" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help=""/>
      <param argument="-max_charge" type="integer" optional="true" min="1" value="3" label="Maximal charge state features should be search fo" help=""/>
      <param argument="-intensity_threshold" type="float" optional="true" min="-1.0" value="-1.0" label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation" help=""/>
      <param argument="-max_isotope" type="integer" optional="true" min="2" value="3" label="Max isotope of the isotope distribution to be considered" help=""/>
      <param argument="-expansion_range" type="float" optional="true" min="0.0" value="5.0" label="The range that is used to extend the isotope distribution with null intensity peaks in Th" help=""/>
      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="feature_out_FLAG">feature_out (Output featureXML file, only written if given, skipped otherwise)</option>
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
    <data name="feature_out" label="${tool.name} on ${on_string}: feature_out" format="featurexml">
      <filter>OPTIONAL_OUTPUTS is not None and "feature_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests><!-- TODO -->
</tests>
  <help><![CDATA[Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.


For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_ERPairFinder.html]]></help>
  <expand macro="references"/>
</tool>