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comparison PrecursorMassCorrector.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="PrecursorMassCorrector" name="PrecursorMassCorrector" version="2.0.0">
3 <description>Corrects the precursor entries of MS/MS spectra, by using MS1 information.</description>
4 <macros>
5 <token name="@EXECUTABLE@">PrecursorMassCorrector</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>PrecursorMassCorrector
11
12 #if $param_in:
13 -in $param_in
14 #end if
15 #if $param_out:
16 -out $param_out
17 #end if
18 #if $param_feature_in:
19 -feature_in $param_feature_in
20 #end if
21 #if $param_precursor_mass_tolerance:
22 -precursor_mass_tolerance $param_precursor_mass_tolerance
23 #end if
24 -threads \${GALAXY_SLOTS:-24}
25 #if $adv_opts.adv_opts_selector=='advanced':
26 #if $adv_opts.param_max_charge:
27 -max_charge $adv_opts.param_max_charge
28 #end if
29 #if $adv_opts.param_intensity_threshold:
30 -intensity_threshold $adv_opts.param_intensity_threshold
31 #end if
32 #if $adv_opts.param_force:
33 -force
34 #end if
35 #end if
36 </command>
37 <inputs>
38 <param name="param_in" type="data" format="mzml" optional="False" label="Input mzML file containing the spectra" help="(-in) "/>
39 <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 &lt;br&gt;will be matched to the feature m/z values if possible" help="(-feature_in) "/>
40 <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; &lt;br&gt;this value should be set to the instruments selection window" help="(-precursor_mass_tolerance) "/>
41 <expand macro="advanced_options">
42 <param name="param_max_charge" type="integer" value="3" label="Maximal charge that should be assumed for precursor peaks" help="(-max_charge) "/>
43 <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) "/>
44 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
45 </expand>
46 </inputs>
47 <outputs>
48 <data name="param_out" format="mzml"/>
49 </outputs>
50 <help>**What it does**
51
52 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 <expand macro="references"/>
57 </tool>