Mercurial > repos > galaxyp > openms_spectrafilterparentpeakmower

comparison SpectraFilterParentPeakMower.xml @ 0:509659eeec69 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 12:29:26 -0500
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children 8a9e7a1ece60
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-1:000000000000 0:509659eeec69
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: [Identification]-->
4 <tool id="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="2.1.0">
5 <description>Applies thresholdfilter to peak spectra.</description>
6 <macros>
7 <token name="@EXECUTABLE@">SpectraFilterParentPeakMower</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>SpectraFilterParentPeakMower
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_algorithm_window_size:
22 -algorithm:window_size $param_algorithm_window_size
23 #end if
24 #if $param_algorithm_default_charge:
25 -algorithm:default_charge $param_algorithm_default_charge
26 #end if
27 #if $param_algorithm_consider_NH3_loss:
28 -algorithm:consider_NH3_loss $param_algorithm_consider_NH3_loss
29 #end if
30 #if $param_algorithm_consider_H2O_loss:
31 -algorithm:consider_H2O_loss $param_algorithm_consider_H2O_loss
32 #end if
33 #if $adv_opts.adv_opts_selector=='advanced':
34 #if $adv_opts.param_force:
35 -force
36 #end if
37 #if $adv_opts.param_algorithm_clean_all_charge_states:
38 -algorithm:clean_all_charge_states $adv_opts.param_algorithm_clean_all_charge_states
39 #end if
40 #if $adv_opts.param_algorithm_reduce_by_factor:
41 -algorithm:reduce_by_factor $adv_opts.param_algorithm_reduce_by_factor
42 #end if
43 #if $adv_opts.param_algorithm_factor:
44 -algorithm:factor $adv_opts.param_algorithm_factor
45 #end if
46 #if $adv_opts.param_algorithm_set_to_zero:
47 -algorithm:set_to_zero $adv_opts.param_algorithm_set_to_zero
48 #end if
49 #end if
50 </command>
51 <inputs>
52 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
53 <param name="param_algorithm_window_size" type="float" value="2.0" label="The size of the m/z window where the peaks are removed, +/- window_size" help="(-window_size) "/>
54 <param name="param_algorithm_default_charge" type="integer" value="2" label="If the precursor has no charge set, the default charge is assumed" help="(-default_charge) "/>
55 <param name="param_algorithm_consider_NH3_loss" type="integer" value="1" label="Whether NH3 loss peaks from the precursor should be removed" help="(-consider_NH3_loss) "/>
56 <param name="param_algorithm_consider_H2O_loss" type="integer" value="1" label="Whether H2O loss peaks from the precursor should be removed" help="(-consider_H2O_loss) "/>
57 <expand macro="advanced_options">
58 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
59 <param name="param_algorithm_clean_all_charge_states" type="integer" value="1" label="Set to 1 if precursor ions of all possible charge states should be removed" help="(-clean_all_charge_states) "/>
60 <param name="param_algorithm_reduce_by_factor" type="integer" value="0" label="Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0)" help="(-reduce_by_factor) "/>
61 <param name="param_algorithm_factor" type="float" value="1000.0" label="Factor which is used to reduce the intensities if 'reduce_by_factor' is selected" help="(-factor) "/>
62 <param name="param_algorithm_set_to_zero" type="integer" value="1" label="Reduce the intensities of the precursor and related ions to zero" help="(-set_to_zero) "/>
63 </expand>
64 </inputs>
65 <outputs>
66 <data name="param_out" format="mzml"/>
67 </outputs>
68 <help>Applies thresholdfilter to peak spectra.
69
70
71 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterParentPeakMower.html</help>
72 </tool>