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comparison SpectraFilterNormalizer.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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-1:000000000000 0:3070d71e0e5c
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="SpectraFilterNormalizer" name="SpectraFilterNormalizer" version="2.0.0">
3 <description>Applies thresholdfilter to peak spectra.</description>
4 <macros>
5 <token name="@EXECUTABLE@">SpectraFilterNormalizer</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>SpectraFilterNormalizer
11
12 #if $param_in:
13 -in $param_in
14 #end if
15 #if $param_out:
16 -out $param_out
17 #end if
18 -threads \${GALAXY_SLOTS:-24}
19 #if $param_algorithm_method:
20 -algorithm:method
21 #if " " in str($param_algorithm_method):
22 "$param_algorithm_method"
23 #else
24 $param_algorithm_method
25 #end if
26 #end if
27 #if $adv_opts.adv_opts_selector=='advanced':
28 #if $adv_opts.param_force:
29 -force
30 #end if
31 #end if
32 </command>
33 <inputs>
34 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
35 <param name="param_algorithm_method" type="select" optional="True" value="to_one" label="Normalize by deviding though the TIC ('to_TIC') or normalize to max intensity of one ('to_one')" help="(-method) ">
36 <option value="to_one">to_one</option>
37 <option value="to_TIC">to_TIC</option>
38 </param>
39 <expand macro="advanced_options">
40 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
41 </expand>
42 </inputs>
43 <outputs>
44 <data name="param_out" format="mzml"/>
45 </outputs>
46 <help>**What it does**
47
48 Applies thresholdfilter to peak spectra.
49
50
51 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterNormalizer.html</help>
52 <expand macro="references"/>
53 </tool>