Mercurial > repos > galaxyp > openms_erpairfinder

comparison ERPairFinder.xml @ 16:3d043a92c582 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 21:34:13 +0000
parents d6ef464ff66b
children
comparison
equal deleted inserted replaced
15:d6ef464ff66b 16:3d043a92c582
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: [Utilities]--> 2 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="ERPairFinder" name="ERPairFinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <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> 4 <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">ERPairFinder</token> 6 <token name="@EXECUTABLE@">ERPairFinder</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($in.ext)' &&
19 mkdir pair_in && 18 mkdir pair_in &&
20 ln -s '$pair_in' 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)' && 19 cp '$pair_in' 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)' &&
21 mkdir out && 20 mkdir out &&
22 #if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 21 #if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
23 mkdir feature_out && 22 mkdir feature_out &&
24 #end if 23 #end if
25 24
54 <configfiles> 53 <configfiles>
55 <inputs name="args_json" data_style="paths"/> 54 <inputs name="args_json" data_style="paths"/>
56 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 55 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
57 </configfiles> 56 </configfiles>
58 <inputs> 57 <inputs>
59 <param argument="-in" type="data" format="mzml" optional="false" label="Input mzML file containing the ER spectra" help=" select mzml data sets(s)"/> 58 <param argument="-in" type="data" format="mzml" label="Input mzML file containing the ER spectra" help=" select mzml 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)"/> 59 <param argument="-pair_in" type="data" format="txt" label="Pair-file in the format: m/z-light m/z-heavy charge rt" help=" select txt data sets(s)"/>
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=""/> 60 <param argument="-precursor_mass_tolerance" type="float" 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=""/>
62 <expand macro="adv_opts_macro"> 61 <expand macro="adv_opts_macro">
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=""/> 62 <param argument="-RT_tolerance" type="float" 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=""/>
64 <param argument="-max_charge" type="integer" optional="true" min="1" value="3" label="Maximal charge state features should be search fo" help=""/> 63 <param argument="-max_charge" type="integer" min="1" value="3" label="Maximal charge state features should be search fo" 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=""/> 64 <param argument="-intensity_threshold" type="float" min="-1.0" value="-1.0" label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation" 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=""/> 65 <param argument="-max_isotope" type="integer" min="2" value="3" label="Max isotope of the isotope distribution to be considered" 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=""/> 66 <param argument="-expansion_range" type="float" min="0.0" value="5.0" label="The range that is used to extend the isotope distribution with null intensity peaks in Th" help=""/>
68 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 67 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
69 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 68 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
70 <expand macro="list_string_san" name="test"/> 69 <expand macro="list_string_san" name="test"/>
71 </param> 70 </param>
72 </expand> 71 </expand>
73 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 72 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
74 <option value="feature_out_FLAG">feature_out (Output featureXML file, only written if given, skipped otherwise)</option> 73 <option value="feature_out_FLAG">feature_out (Output featureXML file, only written if given, skipped otherwise)</option>
82 </data> 81 </data>
83 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 82 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
84 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 83 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
85 </data> 84 </data>
86 </outputs> 85 </outputs>
87 <tests><!-- TODO --> 86 <tests>
88 </tests> 87 <!-- TODO -->
88 </tests>
89 <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.
90 90
91 91
92 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_ERPairFinder.html]]></help> 92 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ERPairFinder.html]]></help>
93 <expand macro="references"/> 93 <expand macro="references"/>
94 </tool> 94 </tool>