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comparison SpectraFilterParentPeakMower.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
comparison
equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="1.12.0"> 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 <description>Applies thresholdfilter to peak spectra.</description> 3 <!--Proposed Tool Section: [Identification]-->
4 <macros> 4 <tool id="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="2.0.0">
5 <token name="@EXECUTABLE@">SpectraFilterParentPeakMower</token> 5 <description>Applies thresholdfilter to peak spectra.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">SpectraFilterParentPeakMower</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>SpectraFilterParentPeakMower 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>SpectraFilterParentPeakMower
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -threads \${GALAXY_SLOTS:-24} 17 #end if
15 -algorithm:window_size ${param_window_size} 18 #if $param_out:
16 -algorithm:default_charge ${param_default_charge} 19 -out $param_out
17 -algorithm:consider_NH3_loss ${param_consider_NH3_loss} 20 #end if
18 -algorithm:consider_H2O_loss ${param_consider_H2O_loss} 21 -threads \${GALAXY_SLOTS:-24}
22 #if $param_algorithm_window_size:
23 -algorithm:window_size $param_algorithm_window_size
24 #end if
25 #if $param_algorithm_default_charge:
26 -algorithm:default_charge $param_algorithm_default_charge
27 #end if
28 #if $param_algorithm_consider_NH3_loss:
29 -algorithm:consider_NH3_loss $param_algorithm_consider_NH3_loss
30 #end if
31 #if $param_algorithm_consider_H2O_loss:
32 -algorithm:consider_H2O_loss $param_algorithm_consider_H2O_loss
33 #end if
19 #if $adv_opts.adv_opts_selector=='advanced': 34 #if $adv_opts.adv_opts_selector=='advanced':
20 -algorithm:clean_all_charge_states ${adv_opts.param_clean_all_charge_states} 35 #if $adv_opts.param_force:
21 -algorithm:reduce_by_factor ${adv_opts.param_reduce_by_factor} 36 -force
22 -algorithm:factor ${adv_opts.param_factor} 37 #end if
23 -algorithm:set_to_zero ${adv_opts.param_set_to_zero} 38 #if $adv_opts.param_algorithm_clean_all_charge_states:
39 -algorithm:clean_all_charge_states $adv_opts.param_algorithm_clean_all_charge_states
40 #end if
41 #if $adv_opts.param_algorithm_reduce_by_factor:
42 -algorithm:reduce_by_factor $adv_opts.param_algorithm_reduce_by_factor
43 #end if
44 #if $adv_opts.param_algorithm_factor:
45 -algorithm:factor $adv_opts.param_algorithm_factor
46 #end if
47 #if $adv_opts.param_algorithm_set_to_zero:
48 -algorithm:set_to_zero $adv_opts.param_algorithm_set_to_zero
49 #end if
24 #end if 50 #end if
25 </command> 51 </command>
26 <inputs> 52 <inputs>
27 <param name="param_in" type="data" format="mzML" optional="False" label="input file " help="(-in)"/> 53 <param format="mzml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
28 <param name="param_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 help="(-window_size) " label="The size of the m/z window where the peaks are removed, +/- window_size" name="param_algorithm_window_size" type="float" value="2.0"/>
29 <param name="param_default_charge" type="integer" value="2" label="If the precursor has no charge set, the default charge is assumed." help="(-default_charge)"/> 55 <param help="(-default_charge) " label="If the precursor has no charge set, the default charge is assumed" name="param_algorithm_default_charge" type="integer" value="2"/>
30 <param name="param_consider_NH3_loss" type="integer" value="1" label="Whether NH3 loss peaks from the precursor should be removed." help="(-consider_NH3_loss)"/> 56 <param help="(-consider_NH3_loss) " label="Whether NH3 loss peaks from the precursor should be removed" name="param_algorithm_consider_NH3_loss" type="integer" value="1"/>
31 <param name="param_consider_H2O_loss" type="integer" value="1" label="Whether H2O loss peaks from the precursor should be removed." help="(-consider_H2O_loss)"/> 57 <param help="(-consider_H2O_loss) " label="Whether H2O loss peaks from the precursor should be removed" name="param_algorithm_consider_H2O_loss" type="integer" value="1"/>
32 <expand macro="advanced_options"> 58 <expand macro="advanced_options">
33 <param name="param_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)"/> 59 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
34 <param name="param_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)"/> 60 <param help="(-clean_all_charge_states) " label="Set to 1 if precursor ions of all possible charge states should be removed" name="param_algorithm_clean_all_charge_states" type="integer" value="1"/>
35 <param name="param_factor" type="float" value="1000.0" label="Factor which is used to reduce the intensities if 'reduce_by_factor' is selected." help="(-factor)"/> 61 <param help="(-reduce_by_factor) " label="Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0)" name="param_algorithm_reduce_by_factor" type="integer" value="0"/>
36 <param name="param_set_to_zero" type="integer" value="1" label="Reduce the intensities of the precursor and related ions to zero." help="(-set_to_zero)"/> 62 <param help="(-factor) " label="Factor which is used to reduce the intensities if 'reduce_by_factor' is selected" name="param_algorithm_factor" type="float" value="1000.0"/>
37 </expand> 63 <param help="(-set_to_zero) " label="Reduce the intensities of the precursor and related ions to zero" name="param_algorithm_set_to_zero" type="integer" value="1"/>
38 </inputs> 64 </expand>
39 <outputs> 65 </inputs>
40 <data name="param_out" label="output file " format="mzML"/> 66 <outputs>
41 </outputs> 67 <data format="mzml" name="param_out"/>
42 <help>**What it does** 68 </outputs>
43 69 <help>Applies thresholdfilter to peak spectra.
44 Applies thresholdfilter to peak spectra.
45 70
46 71
47 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterParentPeakMower.html 72 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterParentPeakMower.html</help>
48 73 </tool>
49 @REFERENCES@
50 </help>
51 </tool>