Mercurial > repos > galaxyp > openms_precursormasscorrector
comparison PrecursorMassCorrector.xml @ 0:7788e4d10cc6 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author | galaxyp |
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date | Wed, 01 Mar 2017 12:52:00 -0500 |
parents | |
children | 5037d5ad9aad |
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-1:000000000000 | 0:7788e4d10cc6 |
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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: [Signal processing and preprocessing]--> | |
4 <tool id="PrecursorMassCorrector" name="PrecursorMassCorrector" version="2.1.0"> | |
5 <description>Corrects the precursor entries of MS/MS spectra, by using MS1 information.</description> | |
6 <macros> | |
7 <token name="@EXECUTABLE@">PrecursorMassCorrector</token> | |
8 <import>macros.xml</import> | |
9 </macros> | |
10 <expand macro="references"/> | |
11 <expand macro="stdio"/> | |
12 <expand macro="requirements"/> | |
13 <command>PrecursorMassCorrector | |
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_feature_in: | |
22 -feature_in $param_feature_in | |
23 #end if | |
24 #if $param_precursor_mass_tolerance: | |
25 -precursor_mass_tolerance $param_precursor_mass_tolerance | |
26 #end if | |
27 #if $adv_opts.adv_opts_selector=='advanced': | |
28 #if $adv_opts.param_max_charge: | |
29 -max_charge $adv_opts.param_max_charge | |
30 #end if | |
31 #if $adv_opts.param_intensity_threshold: | |
32 -intensity_threshold $adv_opts.param_intensity_threshold | |
33 #end if | |
34 #if $adv_opts.param_force: | |
35 -force | |
36 #end if | |
37 #end if | |
38 </command> | |
39 <inputs> | |
40 <param name="param_in" type="data" format="mzml" optional="False" label="Input mzML file containing the spectra" help="(-in) "/> | |
41 <param name="param_feature_in" type="data" format="featurexml" optional="True" label="Input featureXML file, containing features; if set, the MS/MS spectra precursor entries <br>will be matched to the feature m/z values if possible" help="(-feature_in) "/> | |
42 <param name="param_precursor_mass_tolerance" type="float" min="0.0" optional="True" value="1.5" label="Maximal deviation in Th which is acceptable to be corrected; <br>this value should be set to the instruments selection window" help="(-precursor_mass_tolerance) "/> | |
43 <expand macro="advanced_options"> | |
44 <param name="param_max_charge" type="integer" value="3" label="Maximal charge that should be assumed for precursor peaks" help="(-max_charge) "/> | |
45 <param name="param_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="(-intensity_threshold) "/> | |
46 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
47 </expand> | |
48 </inputs> | |
49 <outputs> | |
50 <data name="param_out" format="mzml"/> | |
51 </outputs> | |
52 <help>Corrects the precursor entries of MS/MS spectra, by using MS1 information. | |
53 | |
54 | |
55 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorMassCorrector.html</help> | |
56 </tool> |