Mercurial > repos > galaxyp > openms_metabolitespectralmatcher

comparison MetaboliteSpectralMatcher.xml @ 1:e9729ff6055e draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 08:59:15 -0400
parents d2b1258ee673
children 5df50037ba1f
comparison
equal deleted inserted replaced
0:d2b1258ee673 1:e9729ff6055e
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 CTD2Galaxy.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="2.1.0"> 4 <tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="2.2.0">
5 <description>Find potential HMDB ids within the given mass error window.</description> 5 <description>Perform a spectral library search.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MetaboliteSpectralMatcher</token> 7 <token name="@EXECUTABLE@">MetaboliteSpectralMatcher</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="references"/>
13 <command>MetaboliteSpectralMatcher 13 <command>MetaboliteSpectralMatcher
14 14
15 #if $param_in: 15 #if $param_in:
16 -in $param_in 16 -in $param_in
17 #end if 17 #end if
18 #if $param_database:
19 -database $param_database
20 #end if
18 #if $param_out: 21 #if $param_out:
19 -out $param_out 22 -out $param_out
20 #end if 23 #end if
21 #if $param_algorithm_prec_mass_error_value: 24 #if $param_algorithm_prec_mass_error_value:
22 -algorithm:prec_mass_error_value $param_algorithm_prec_mass_error_value 25 -algorithm:prec_mass_error_value $param_algorithm_prec_mass_error_value
23 #end if 26 #end if
24 #if $param_algorithm_frag_mass_error_value: 27 #if $param_algorithm_frag_mass_error_value:
25 -algorithm:frag_mass_error_value $param_algorithm_frag_mass_error_value 28 -algorithm:frag_mass_error_value $param_algorithm_frag_mass_error_value
26 #end if 29 #end if
27 #if $param_algorithm_mass_error_unit: 30 #if $param_algorithm_mass_error_unit:
28 -algorithm:mass_error_unit $param_algorithm_mass_error_unit 31 -algorithm:mass_error_unit
32 #if " " in str($param_algorithm_mass_error_unit):
33 "$param_algorithm_mass_error_unit"
34 #else
35 $param_algorithm_mass_error_unit
36 #end if
29 #end if 37 #end if
30 #if $param_algorithm_report_mode: 38 #if $param_algorithm_report_mode:
31 -algorithm:report_mode $param_algorithm_report_mode 39 -algorithm:report_mode
40 #if " " in str($param_algorithm_report_mode):
41 "$param_algorithm_report_mode"
42 #else
43 $param_algorithm_report_mode
44 #end if
32 #end if 45 #end if
33 #if $param_algorithm_ionization_mode: 46 #if $param_algorithm_ionization_mode:
34 -algorithm:ionization_mode $param_algorithm_ionization_mode 47 -algorithm:ionization_mode
48 #if " " in str($param_algorithm_ionization_mode):
49 "$param_algorithm_ionization_mode"
50 #else
51 $param_algorithm_ionization_mode
52 #end if
35 #end if 53 #end if
36 #if $adv_opts.adv_opts_selector=='advanced': 54 #if $adv_opts.adv_opts_selector=='advanced':
37 #if $adv_opts.param_force: 55 #if $adv_opts.param_force:
38 -force 56 -force
39 #end if 57 #end if
40 #end if 58 #end if
41 </command> 59 </command>
42 <inputs> 60 <inputs>
43 <param name="param_in" type="data" format="mzml" optional="False" label="mzML file" help="(-in) "/> 61 <param name="param_in" type="data" format="mzml" optional="False" label="Input spectra" help="(-in) "/>
62 <param name="param_database" type="data" format="mzml" optional="True" value="CHEMISTRY/MetaboliteSpectralDB.mzML" label="Default spectral database" help="(-database) "/>
44 <param name="param_algorithm_prec_mass_error_value" type="float" value="100.0" label="Error allowed for precursor ion mass" help="(-prec_mass_error_value) "/> 63 <param name="param_algorithm_prec_mass_error_value" type="float" value="100.0" label="Error allowed for precursor ion mass" help="(-prec_mass_error_value) "/>
45 <param name="param_algorithm_frag_mass_error_value" type="float" value="500.0" label="Error allowed for product ions" help="(-frag_mass_error_value) "/> 64 <param name="param_algorithm_frag_mass_error_value" type="float" value="500.0" label="Error allowed for product ions" help="(-frag_mass_error_value) "/>
46 <param name="param_algorithm_mass_error_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of mass error (ppm or Da)" help="(-mass_error_unit) "> 65 <param name="param_algorithm_mass_error_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of mass error (ppm or Da)" help="(-mass_error_unit) ">
47 <option value="ppm" selected="true">ppm</option> 66 <option value="ppm" selected="true">ppm</option>
48 <option value="Da">Da</option> 67 <option value="Da">Da</option>
60 </expand> 79 </expand>
61 </inputs> 80 </inputs>
62 <outputs> 81 <outputs>
63 <data name="param_out" format="tabular"/> 82 <data name="param_out" format="tabular"/>
64 </outputs> 83 </outputs>
65 <help>Find potential HMDB ids within the given mass error window. 84 <help>Perform a spectral library search.
66 85
67 86
68 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MetaboliteSpectralMatcher.html</help> 87 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MetaboliteSpectralMatcher.html</help>
69 </tool> 88 </tool>