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comparison ERPairFinder.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="ERPairFinder" name="ERPairFinder" version="2.0.0">
3 <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description>
4 <macros>
5 <token name="@EXECUTABLE@">ERPairFinder</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>ERPairFinder
11
12 #if $param_in:
13 -in $param_in
14 #end if
15 #if $param_pair_in:
16 -pair_in $param_pair_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_feature_out:
22 -feature_out $param_feature_out
23 #end if
24 #if $param_precursor_mass_tolerance:
25 -precursor_mass_tolerance $param_precursor_mass_tolerance
26 #end if
27 -threads \${GALAXY_SLOTS:-24}
28 #if $adv_opts.adv_opts_selector=='advanced':
29 #if $adv_opts.param_RT_tolerance:
30 -RT_tolerance $adv_opts.param_RT_tolerance
31 #end if
32 #if $adv_opts.param_max_charge:
33 -max_charge $adv_opts.param_max_charge
34 #end if
35 #if $adv_opts.param_intensity_threshold:
36 -intensity_threshold $adv_opts.param_intensity_threshold
37 #end if
38 #if $adv_opts.param_max_isotope:
39 -max_isotope $adv_opts.param_max_isotope
40 #end if
41 #if $adv_opts.param_expansion_range:
42 -expansion_range $adv_opts.param_expansion_range
43 #end if
44 #if $adv_opts.param_force:
45 -force
46 #end if
47 #end if
48 </command>
49 <inputs>
50 <param name="param_in" type="data" format="mzml" optional="False" label="Input mzML file containing the ER spectra" help="(-in) "/>
51 <param name="param_pair_in" type="data" format="txt" optional="False" label="Pair-file in the format: m/z-light m/z-heavy charge rt" help="(-pair_in) "/>
52 <param name="param_precursor_mass_tolerance" type="float" min="0.0" optional="True" value="0.3" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" help="(-precursor_mass_tolerance) "/>
53 <expand macro="advanced_options">
54 <param name="param_RT_tolerance" type="float" min="1.0" optional="True" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help="(-RT_tolerance) "/>
55 <param name="param_max_charge" type="integer" min="1" optional="True" value="3" label="Maximal charge state features should be search fo" help="(-max_charge) "/>
56 <param name="param_intensity_threshold" type="float" min="-1.0" optional="True" value="-1.0" label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation" help="(-intensity_threshold) "/>
57 <param name="param_max_isotope" type="integer" min="2" optional="True" value="3" label="Max isotope of the isotope distribution to be considered" help="(-max_isotope) "/>
58 <param name="param_expansion_range" type="float" min="0.0" optional="True" value="5.0" label="The range that is used to extend the isotope distribution with null intensity peaks in Th" help="(-expansion_range) "/>
59 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
60 </expand>
61 </inputs>
62 <outputs>
63 <data name="param_out" format="consensusxml"/>
64 <data name="param_feature_out" format="featurexml"/>
65 </outputs>
66 <help>**What it does**
67
68 Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
69
70
71 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_ERPairFinder.html</help>
72 <expand macro="references"/>
73 </tool>