Mercurial > repos > galaxyp > openms_featurefinderisotopewavelet

comparison FeatureFinderIsotopeWavelet.xml @ 9:f838387867c8 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Fri, 17 May 2019 05:00:59 -0400
parents e046e3de64cf
children becf3642c634
comparison
equal deleted inserted replaced
8:ef542d31cf5c 9:f838387867c8
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="references"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements"/>
13 <command>FeatureFinderIsotopeWavelet 13 <command detect_errors="aggressive"><![CDATA[FeatureFinderIsotopeWavelet
14 14
15 #if $param_in: 15 #if $param_in:
16 -in $param_in 16 -in $param_in
17 #end if 17 #end if
18 #if $param_out: 18 #if $param_out:
47 #end if 47 #end if
48 #if $adv_opts.param_algorithm_sweep_line_rt_interleave: 48 #if $adv_opts.param_algorithm_sweep_line_rt_interleave:
49 -algorithm:sweep_line:rt_interleave $adv_opts.param_algorithm_sweep_line_rt_interleave 49 -algorithm:sweep_line:rt_interleave $adv_opts.param_algorithm_sweep_line_rt_interleave
50 #end if 50 #end if
51 #end if 51 #end if
52 </command> 52 ]]></command>
53 <inputs> 53 <inputs>
54 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/> 54 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
55 <param name="param_algorithm_max_charge" type="integer" min="1" optional="True" value="3" label="The maximal charge state to be considered" help="(-max_charge) "/> 55 <param name="param_algorithm_max_charge" type="integer" min="1" optional="True" value="3" label="The maximal charge state to be considered" help="(-max_charge) "/>
56 <param name="param_algorithm_intensity_threshold" type="float" value="-1.0" label="The final threshold t' is build upon the formula: t' = av+t*sd, where t is the intensity_threshold, av the average intensity within the wavelet transformed signal and sd the standard deviation of the transform" help="(-intensity_threshold) If you set intensity_threshold=-1, t' will be zero. &lt;br&gt;As the 'optimal' value for this parameter is highly data dependent, we would recommend to start with -1, which will also extract features with very low signal-to-noise ratio. Subsequently, one might increase the threshold to find an optimized trade-off between false positives and true positives. Depending on the dynamic range of your spectra, suitable value ranges include: -1, [0:10], and if your data features even very high intensity values, t can also adopt values up to around 30. Please note that this parameter is not of an integer type, s.t. you can also use t:=0.1, e.g"/> 56 <param name="param_algorithm_intensity_threshold" type="float" value="-1.0" label="The final threshold t' is build upon the formula: t' = av+t*sd, where t is the intensity_threshold, av the average intensity within the wavelet transformed signal and sd the standard deviation of the transform" help="(-intensity_threshold) If you set intensity_threshold=-1, t' will be zero. &lt;br&gt;As the 'optimal' value for this parameter is highly data dependent, we would recommend to start with -1, which will also extract features with very low signal-to-noise ratio. Subsequently, one might increase the threshold to find an optimized trade-off between false positives and true positives. Depending on the dynamic range of your spectra, suitable value ranges include: -1, [0:10], and if your data features even very high intensity values, t can also adopt values up to around 30. Please note that this parameter is not of an integer type, s.t. you can also use t:=0.1, e.g"/>
57 <param name="param_algorithm_hr_data" display="radio" type="boolean" truevalue="-algorithm:hr_data" falsevalue="" checked="false" optional="True" label="Must be true in case of high-resolution data, i.e. for spectra featuring large m/z-gaps (present in FTICR and Orbitrap data," help="(-hr_data) e.g.). Please check a single MS scan out of your recording, if you are unsure"/> 57 <param name="param_algorithm_hr_data" display="radio" type="boolean" truevalue="-algorithm:hr_data" falsevalue="" checked="false" optional="True" label="Must be true in case of high-resolution data, i.e. for spectra featuring large m/z-gaps (present in FTICR and Orbitrap data," help="(-hr_data) e.g.). Please check a single MS scan out of your recording, if you are unsure"/>
71 <data name="param_out" format="featurexml"/> 71 <data name="param_out" format="featurexml"/>
72 </outputs> 72 </outputs>
73 <help>Detects two-dimensional features in LC-MS data. 73 <help>Detects two-dimensional features in LC-MS data.
74 74
75 75
76 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderIsotopeWavelet.html</help> 76 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureFinderIsotopeWavelet.html</help>
77 </tool> 77 </tool>