Mercurial > repos > galaxyp > openms_spectrafilterparentpeakmower
diff SpectraFilterParentPeakMower.xml @ 0:509659eeec69 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author | galaxyp |
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date | Wed, 01 Mar 2017 12:29:26 -0500 |
parents | |
children | 8a9e7a1ece60 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SpectraFilterParentPeakMower.xml Wed Mar 01 12:29:26 2017 -0500 @@ -0,0 +1,72 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Identification]--> +<tool id="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="2.1.0"> + <description>Applies thresholdfilter to peak spectra.</description> + <macros> + <token name="@EXECUTABLE@">SpectraFilterParentPeakMower</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>SpectraFilterParentPeakMower + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_algorithm_window_size: + -algorithm:window_size $param_algorithm_window_size +#end if +#if $param_algorithm_default_charge: + -algorithm:default_charge $param_algorithm_default_charge +#end if +#if $param_algorithm_consider_NH3_loss: + -algorithm:consider_NH3_loss $param_algorithm_consider_NH3_loss +#end if +#if $param_algorithm_consider_H2O_loss: + -algorithm:consider_H2O_loss $param_algorithm_consider_H2O_loss +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_clean_all_charge_states: + -algorithm:clean_all_charge_states $adv_opts.param_algorithm_clean_all_charge_states +#end if + #if $adv_opts.param_algorithm_reduce_by_factor: + -algorithm:reduce_by_factor $adv_opts.param_algorithm_reduce_by_factor +#end if + #if $adv_opts.param_algorithm_factor: + -algorithm:factor $adv_opts.param_algorithm_factor +#end if + #if $adv_opts.param_algorithm_set_to_zero: + -algorithm:set_to_zero $adv_opts.param_algorithm_set_to_zero +#end if +#end if +</command> + <inputs> + <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/> + <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) "/> + <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) "/> + <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) "/> + <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) "/> + <expand macro="advanced_options"> + <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + <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) "/> + <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) "/> + <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) "/> + <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) "/> + </expand> + </inputs> + <outputs> + <data name="param_out" format="mzml"/> + </outputs> + <help>Applies thresholdfilter to peak spectra. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterParentPeakMower.html</help> +</tool>