Mercurial > repos > galaxyp > openms_metabolitespectralmatcher

comparison MetaboliteSpectralMatcher.xml @ 0:d2b1258ee673 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:16:51 -0500
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-1:000000000000 0:d2b1258ee673
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.-->
3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="2.1.0">
5 <description>Find potential HMDB ids within the given mass error window.</description>
6 <macros>
7 <token name="@EXECUTABLE@">MetaboliteSpectralMatcher</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>MetaboliteSpectralMatcher
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_algorithm_prec_mass_error_value:
22 -algorithm:prec_mass_error_value $param_algorithm_prec_mass_error_value
23 #end if
24 #if $param_algorithm_frag_mass_error_value:
25 -algorithm:frag_mass_error_value $param_algorithm_frag_mass_error_value
26 #end if
27 #if $param_algorithm_mass_error_unit:
28 -algorithm:mass_error_unit $param_algorithm_mass_error_unit
29 #end if
30 #if $param_algorithm_report_mode:
31 -algorithm:report_mode $param_algorithm_report_mode
32 #end if
33 #if $param_algorithm_ionization_mode:
34 -algorithm:ionization_mode $param_algorithm_ionization_mode
35 #end if
36 #if $adv_opts.adv_opts_selector=='advanced':
37 #if $adv_opts.param_force:
38 -force
39 #end if
40 #end if
41 </command>
42 <inputs>
43 <param name="param_in" type="data" format="mzml" optional="False" label="mzML file" help="(-in) "/>
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) "/>
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) "/>
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) ">
47 <option value="ppm" selected="true">ppm</option>
48 <option value="Da">Da</option>
49 </param>
50 <param name="param_algorithm_report_mode" display="radio" type="select" optional="False" value="top3" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="(-report_mode) ">
51 <option value="top3" selected="true">top3</option>
52 <option value="best">best</option>
53 </param>
54 <param name="param_algorithm_ionization_mode" display="radio" type="select" optional="False" value="positive" label="Positive or negative ionization mode?" help="(-ionization_mode) ">
55 <option value="positive" selected="true">positive</option>
56 <option value="negative">negative</option>
57 </param>
58 <expand macro="advanced_options">
59 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
60 </expand>
61 </inputs>
62 <outputs>
63 <data name="param_out" format="tabular"/>
64 </outputs>
65 <help>Find potential HMDB ids within the given mass error window.
66
67
68 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MetaboliteSpectralMatcher.html</help>
69 </tool>