Mercurial > repos > galaxyp > openms_erpairfinder

comparison ERPairFinder.xml @ 0:434e2afd1d8a draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:57:35 -0500
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children 1cc2379045c3
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-1:000000000000 0:434e2afd1d8a
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="ERPairFinder" name="ERPairFinder" version="2.1.0">
5 <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description>
6 <macros>
7 <token name="@EXECUTABLE@">ERPairFinder</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>ERPairFinder
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_pair_in:
19 -pair_in $param_pair_in
20 #end if
21 #if $param_out:
22 -out $param_out
23 #end if
24 #if $param_feature_out:
25 -feature_out $param_feature_out
26 #end if
27 #if $param_precursor_mass_tolerance:
28 -precursor_mass_tolerance $param_precursor_mass_tolerance
29 #end if
30 #if $adv_opts.adv_opts_selector=='advanced':
31 #if $adv_opts.param_RT_tolerance:
32 -RT_tolerance $adv_opts.param_RT_tolerance
33 #end if
34 #if $adv_opts.param_max_charge:
35 -max_charge $adv_opts.param_max_charge
36 #end if
37 #if $adv_opts.param_intensity_threshold:
38 -intensity_threshold $adv_opts.param_intensity_threshold
39 #end if
40 #if $adv_opts.param_max_isotope:
41 -max_isotope $adv_opts.param_max_isotope
42 #end if
43 #if $adv_opts.param_expansion_range:
44 -expansion_range $adv_opts.param_expansion_range
45 #end if
46 #if $adv_opts.param_force:
47 -force
48 #end if
49 #end if
50 </command>
51 <inputs>
52 <param name="param_in" type="data" format="mzml" optional="False" label="Input mzML file containing the ER spectra" help="(-in) "/>
53 <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) "/>
54 <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) "/>
55 <expand macro="advanced_options">
56 <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) "/>
57 <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) "/>
58 <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) "/>
59 <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) "/>
60 <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) "/>
61 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
62 </expand>
63 </inputs>
64 <outputs>
65 <data name="param_out" format="consensusxml"/>
66 <data name="param_feature_out" format="featurexml"/>
67 </outputs>
68 <help>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 </tool>