Mercurial > repos > galaxyp > openms_precursormasscorrector

comparison PrecursorMassCorrector.xml @ 13:b71e9103d269 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:28:46 +0000
parents 35123b3fe2f2
children
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equal deleted inserted replaced
12:35123b3fe2f2 13:b71e9103d269
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [Mass Correction and Calibration]-->
4 <tool id="PrecursorMassCorrector" name="PrecursorMassCorrector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <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> 4 <description>Corrects the precursor entries of MS/MS spectra, by using MS1 information</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">PrecursorMassCorrector</token> 6 <token name="@EXECUTABLE@">PrecursorMassCorrector</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 #if $feature_in: 19 #if $feature_in:
21 mkdir feature_in && 20 mkdir feature_in &&
22 ln -s '$feature_in' 'feature_in/${re.sub("[^\w\-_]", "_", $feature_in.element_identifier)}.$gxy2omsext($feature_in.ext)' && 21 cp '$feature_in' 'feature_in/${re.sub("[^\w\-_]", "_", $feature_in.element_identifier)}.$gxy2omsext($feature_in.ext)' &&
23 #end if 22 #end if
24 23
25 ## Main program call 24 ## Main program call
26 25
27 set -o pipefail && 26 set -o pipefail &&
45 <configfiles> 44 <configfiles>
46 <inputs name="args_json" data_style="paths"/> 45 <inputs name="args_json" data_style="paths"/>
47 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 46 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
48 </configfiles> 47 </configfiles>
49 <inputs> 48 <inputs>
50 <param argument="-in" type="data" format="mzml" optional="false" label="Input mzML file containing the spectra" help=" select mzml data sets(s)"/> 49 <param argument="-in" type="data" format="mzml" label="Input mzML file containing the spectra" help=" select mzml 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)"/> 50 <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)"/>
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"/> 51 <param argument="-precursor_mass_tolerance" type="float" 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"/>
53 <expand macro="adv_opts_macro"> 52 <expand macro="adv_opts_macro">
54 <param argument="-max_charge" type="integer" optional="true" value="3" label="Maximal charge that should be assumed for precursor peaks" help=""/> 53 <param argument="-max_charge" type="integer" value="3" label="Maximal charge that should be assumed for precursor peaks" 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=""/> 54 <param argument="-intensity_threshold" type="float" value="-1.0" label="Intensity threshold value for isotope wavelet feature finder, please look at the documentation of the class for details" help=""/>
56 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 55 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
57 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 56 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
58 <expand macro="list_string_san" name="test"/> 57 <expand macro="list_string_san" name="test"/>
59 </param> 58 </param>
60 </expand> 59 </expand>
61 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 60 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
62 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 61 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
66 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 65 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
67 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 66 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
68 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 67 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
69 </data> 68 </data>
70 </outputs> 69 </outputs>
71 <tests><!-- TOPP_PrecursorMassCorrector_1 --> 70 <tests>
71 <!-- TOPP_PrecursorMassCorrector_1 -->
72 <test expect_num_outputs="2"> 72 <test expect_num_outputs="2">
73 <section name="adv_opts"> 73 <section name="adv_opts">
74 <param name="max_charge" value="3"/> 74 <param name="max_charge" value="3"/>
75 <param name="intensity_threshold" value="-1.0"/> 75 <param name="intensity_threshold" value="-1.0"/>
76 <param name="force" value="false"/> 76 <param name="force" value="false"/>
77 <param name="test" value="true"/> 77 <param name="test" value="true"/>
78 </section> 78 </section>
79 <param name="in" value="PrecursorMassCorrector_1_input.mzML"/> 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"/> 80 <output name="out" value="PrecursorMassCorrector_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
81 <param name="precursor_mass_tolerance" value="1.5"/> 81 <param name="precursor_mass_tolerance" value="1.5"/>
82 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 82 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83 <output name="ctd_out" ftype="xml"> 83 <output name="ctd_out" ftype="xml">
84 <assert_contents> 84 <assert_contents>
85 <is_valid_xml/> 85 <is_valid_xml/>
86 </assert_contents> 86 </assert_contents>
87 </output> 87 </output>
88 <assert_stdout>
89 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
90 </assert_stdout>
88 </test> 91 </test>
89 </tests> 92 </tests>
90 <help><![CDATA[Corrects the precursor entries of MS/MS spectra, by using MS1 information. 93 <help><![CDATA[Corrects the precursor entries of MS/MS spectra, by using MS1 information.
91 94
92 95
93 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PrecursorMassCorrector.html]]></help> 96 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PrecursorMassCorrector.html]]></help>
94 <expand macro="references"/> 97 <expand macro="references"/>
95 </tool> 98 </tool>