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comparison SpectraFilterWindowMower.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="SpectraFilterWindowMower" name="SpectraFilterWindowMower" version="2.0.0">
3 <description>Applies thresholdfilter to peak spectra.</description>
4 <macros>
5 <token name="@EXECUTABLE@">SpectraFilterWindowMower</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>SpectraFilterWindowMower
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_windowsize:
20 -algorithm:windowsize $param_algorithm_windowsize
21 #end if
22 #if $param_algorithm_peakcount:
23 -algorithm:peakcount $param_algorithm_peakcount
24 #end if
25 #if $param_algorithm_movetype:
26 -algorithm:movetype
27 #if " " in str($param_algorithm_movetype):
28 "$param_algorithm_movetype"
29 #else
30 $param_algorithm_movetype
31 #end if
32 #end if
33 #if $adv_opts.adv_opts_selector=='advanced':
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 file" help="(-in) "/>
41 <param name="param_algorithm_windowsize" type="float" value="50.0" label="The size of the sliding window along the m/z axis" help="(-windowsize) "/>
42 <param name="param_algorithm_peakcount" type="integer" value="2" label="The number of peaks that should be kept" help="(-peakcount) "/>
43 <param name="param_algorithm_movetype" type="select" optional="True" value="slide" label="Whether sliding window (one peak steps) or jumping window (window size steps) should be used" help="(-movetype) ">
44 <option value="slide">slide</option>
45 <option value="jump">jump</option>
46 </param>
47 <expand macro="advanced_options">
48 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
49 </expand>
50 </inputs>
51 <outputs>
52 <data name="param_out" format="mzml"/>
53 </outputs>
54 <help>**What it does**
55
56 Applies thresholdfilter to peak spectra.
57
58
59 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterWindowMower.html</help>
60 <expand macro="references"/>
61 </tool>