Mercurial > repos > galaxyp > openms_precursormasscorrector

comparison PrecursorMassCorrector.xml @ 12:35123b3fe2f2 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 18:58:17 +0000
parents e15d84652dba
children
comparison
equal deleted inserted replaced
11:7605adf55b7c 12:35123b3fe2f2
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: [Signal processing and preprocessing]--> 3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <tool id="PrecursorMassCorrector" name="PrecursorMassCorrector" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="PrecursorMassCorrector" name="PrecursorMassCorrector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Corrects the precursor entries of MS/MS spectra, by using MS1 information.</description> 5 <description>Corrects the precursor entries of MS/MS spectra, by using MS1 information.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">PrecursorMassCorrector</token> 7 <token name="@EXECUTABLE@">PrecursorMassCorrector</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@
47 <configfiles> 45 <configfiles>
48 <inputs name="args_json" data_style="paths"/> 46 <inputs name="args_json" data_style="paths"/>
49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 47 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
50 </configfiles> 48 </configfiles>
51 <inputs> 49 <inputs>
52 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input mzML file containing the spectra" help=" select mzml data sets(s)"/> 50 <param argument="-in" type="data" format="mzml" optional="false" label="Input mzML file containing the spectra" help=" select mzml data sets(s)"/>
53 <param name="feature_in" argument="-feature_in" type="data" format="featurexml" optional="true" label="Input featureXML file, containing features; if set, the MS/MS spectra precursor entries" help="will be matched to the feature m/z values if possible select featurexml data sets(s)"/> 51 <param argument="-feature_in" type="data" format="featurexml" optional="true" label="Input featureXML file, containing features; if set, the MS/MS spectra precursor entries" help="will be matched to the feature m/z values if possible select featurexml data sets(s)"/>
54 <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" min="0.0" value="1.5" label="Maximal deviation in Th which is acceptable to be corrected;" help="this value should be set to the instruments selection window"/> 52 <param argument="-precursor_mass_tolerance" type="float" optional="true" min="0.0" value="1.5" label="Maximal deviation in Th which is acceptable to be corrected;" help="this value should be set to the instruments selection window"/>
55 <expand macro="adv_opts_macro"> 53 <expand macro="adv_opts_macro">
56 <param name="max_charge" argument="-max_charge" type="integer" optional="true" value="3" label="Maximal charge that should be assumed for precursor peaks" help=""/> 54 <param argument="-max_charge" type="integer" optional="true" value="3" label="Maximal charge that should be assumed for precursor peaks" help=""/>
57 <param name="intensity_threshold" argument="-intensity_threshold" type="float" optional="true" value="-1.0" label="Intensity threshold value for isotope wavelet feature finder, please look at the documentation of the class for details" help=""/> 55 <param argument="-intensity_threshold" type="float" optional="true" value="-1.0" label="Intensity threshold value for isotope wavelet feature finder, please look at the documentation of the class for details" help=""/>
58 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 56 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
59 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 57 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
60 <expand macro="list_string_san"/> 58 <expand macro="list_string_san" name="test"/>
61 </param> 59 </param>
62 </expand> 60 </expand>
63 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 61 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
64 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 62 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
65 </param> 63 </param>
68 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 66 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 67 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 68 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
71 </data> 69 </data>
72 </outputs> 70 </outputs>
73 <tests> 71 <tests><!-- TOPP_PrecursorMassCorrector_1 -->
74 <expand macro="autotest_PrecursorMassCorrector"/> 72 <test expect_num_outputs="2">
75 <expand macro="manutest_PrecursorMassCorrector"/> 73 <section name="adv_opts">
74 <param name="max_charge" value="3"/>
75 <param name="intensity_threshold" value="-1.0"/>
76 <param name="force" value="false"/>
77 <param name="test" value="true"/>
78 </section>
79 <param name="in" value="PrecursorMassCorrector_1_input.mzML"/>
80 <output name="out" file="PrecursorMassCorrector_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
81 <param name="precursor_mass_tolerance" value="1.5"/>
82 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83 <output name="ctd_out" ftype="xml">
84 <assert_contents>
85 <is_valid_xml/>
86 </assert_contents>
87 </output>
88 </test>
76 </tests> 89 </tests>
77 <help><![CDATA[Corrects the precursor entries of MS/MS spectra, by using MS1 information. 90 <help><![CDATA[Corrects the precursor entries of MS/MS spectra, by using MS1 information.
78 91
79 92
80 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_PrecursorMassCorrector.html]]></help> 93 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PrecursorMassCorrector.html]]></help>
81 <expand macro="references"/> 94 <expand macro="references"/>
82 </tool> 95 </tool>