Mercurial > repos > galaxyp > openms_erpairfinder

comparison ERPairFinder.xml @ 15:d6ef464ff66b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:06:06 +0000
parents e5e2b0d57f1d
children 3d043a92c582
comparison
equal deleted inserted replaced
14:c7a072fe0088 15:d6ef464ff66b
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="ERPairFinder" name="ERPairFinder" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="ERPairFinder" name="ERPairFinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description> 5 <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">ERPairFinder</token> 7 <token name="@EXECUTABLE@">ERPairFinder</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
56 <configfiles> 54 <configfiles>
57 <inputs name="args_json" data_style="paths"/> 55 <inputs name="args_json" data_style="paths"/>
58 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 56 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
59 </configfiles> 57 </configfiles>
60 <inputs> 58 <inputs>
61 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input mzML file containing the ER spectra" help=" select mzml data sets(s)"/> 59 <param argument="-in" type="data" format="mzml" optional="false" label="Input mzML file containing the ER spectra" help=" select mzml data sets(s)"/>
62 <param name="pair_in" 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)"/> 60 <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)"/>
63 <param name="precursor_mass_tolerance" 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=""/> 61 <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=""/>
64 <expand macro="adv_opts_macro"> 62 <expand macro="adv_opts_macro">
65 <param name="RT_tolerance" 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=""/> 63 <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=""/>
66 <param name="max_charge" argument="-max_charge" type="integer" optional="true" min="1" value="3" label="Maximal charge state features should be search fo" help=""/> 64 <param argument="-max_charge" type="integer" optional="true" min="1" value="3" label="Maximal charge state features should be search fo" help=""/>
67 <param name="intensity_threshold" 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=""/> 65 <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=""/>
68 <param name="max_isotope" argument="-max_isotope" type="integer" optional="true" min="2" value="3" label="Max isotope of the isotope distribution to be considered" help=""/> 66 <param argument="-max_isotope" type="integer" optional="true" min="2" value="3" label="Max isotope of the isotope distribution to be considered" help=""/>
69 <param name="expansion_range" 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=""/> 67 <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=""/>
70 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 68 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
71 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 69 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
72 <expand macro="list_string_san"/> 70 <expand macro="list_string_san" name="test"/>
73 </param> 71 </param>
74 </expand> 72 </expand>
75 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 73 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
76 <option value="feature_out_FLAG">feature_out (Output featureXML file, only written if given, skipped otherwise)</option> 74 <option value="feature_out_FLAG">feature_out (Output featureXML file, only written if given, skipped otherwise)</option>
77 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 75 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
84 </data> 82 </data>
85 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 83 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
86 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 84 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
87 </data> 85 </data>
88 </outputs> 86 </outputs>
89 <tests> 87 <tests><!-- TODO -->
90 <expand macro="autotest_ERPairFinder"/> 88 </tests>
91 <expand macro="manutest_ERPairFinder"/>
92 </tests>
93 <help><![CDATA[Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans. 89 <help><![CDATA[Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
94 90
95 91
96 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_ERPairFinder.html]]></help> 92 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_ERPairFinder.html]]></help>
97 <expand macro="references"/> 93 <expand macro="references"/>
98 </tool> 94 </tool>