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comparison FeatureFinderMRM.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="FeatureFinderMRM" name="FeatureFinderMRM" version="2.0.0">
3 <description>Detects two-dimensional features in LC-MS data.</description>
4 <macros>
5 <token name="@EXECUTABLE@">FeatureFinderMRM</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>FeatureFinderMRM
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_min_rt_distance:
20 -algorithm:min_rt_distance $param_algorithm_min_rt_distance
21 #end if
22 #if $param_algorithm_min_signal_to_noise_ratio:
23 -algorithm:min_signal_to_noise_ratio $param_algorithm_min_signal_to_noise_ratio
24 #end if
25 #if $adv_opts.adv_opts_selector=='advanced':
26 #if $adv_opts.param_force:
27 -force
28 #end if
29 #if $adv_opts.param_algorithm_min_num_peaks_per_feature:
30 -algorithm:min_num_peaks_per_feature $adv_opts.param_algorithm_min_num_peaks_per_feature
31 #end if
32 #if $adv_opts.param_algorithm_write_debug_files:
33 -algorithm:write_debug_files
34 #end if
35 #if $adv_opts.param_algorithm_resample_traces:
36 -algorithm:resample_traces
37 #end if
38 #if $adv_opts.param_algorithm_write_debuginfo:
39 -algorithm:write_debuginfo
40 #end if
41 #end if
42 </command>
43 <inputs>
44 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
45 <param name="param_algorithm_min_rt_distance" type="float" min="0.0" optional="True" value="10.0" label="Minimal distance of MRM features in seconds" help="(-min_rt_distance) "/>
46 <param name="param_algorithm_min_signal_to_noise_ratio" type="float" min="0.0" optional="True" value="2.0" label="Minimal S/N ratio a peak must have to be taken into account" help="(-min_signal_to_noise_ratio) Set to zero if the MRM-traces contains mostly signals, and no noise"/>
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 <param name="param_algorithm_min_num_peaks_per_feature" type="integer" min="1" optional="True" value="5" label="Minimal number of peaks which are needed for a single feature" help="(-min_num_peaks_per_feature) "/>
50 <param name="param_algorithm_write_debug_files" type="boolean" truevalue="-algorithm:write_debug_files" falsevalue="" checked="false" optional="True" label="If set to true, for each feature a plot will be created, in the subdirectory 'debug'" help="(-write_debug_files) "/>
51 <param name="param_algorithm_resample_traces" type="boolean" truevalue="-algorithm:resample_traces" falsevalue="" checked="false" optional="True" label="If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimension" help="(-resample_traces) "/>
52 <param name="param_algorithm_write_debuginfo" type="boolean" truevalue="-algorithm:write_debuginfo" falsevalue="" checked="false" optional="True" label="If set to true, debug messages are written, the output can be somewhat lengthy" help="(-write_debuginfo) "/>
53 </expand>
54 </inputs>
55 <outputs>
56 <data name="param_out" format="featurexml"/>
57 </outputs>
58 <help>**What it does**
59
60 Detects two-dimensional features in LC-MS data.
61
62
63 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMRM.html</help>
64 <expand macro="references"/>
65 </tool>