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comparison FeatureFinderIsotopeWavelet.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="FeatureFinderIsotopeWavelet" name="FeatureFinderIsotopeWavelet" 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>Detects two-dimensional features in LC-MS data.</description> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <macros> 4 <tool id="FeatureFinderIsotopeWavelet" name="FeatureFinderIsotopeWavelet" version="2.0.0">
5 <token name="@EXECUTABLE@">FeatureFinderIsotopeWavelet</token> 5 <description>Detects two-dimensional features in LC-MS data.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">FeatureFinderIsotopeWavelet</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>FeatureFinderIsotopeWavelet 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FeatureFinderIsotopeWavelet
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:max_charge ${param_max_charge} 18 #if $param_out:
16 -algorithm:intensity_threshold ${param_intensity_threshold} 19 -out $param_out
17 ${param_hr_data} 20 #end if
21 -threads \${GALAXY_SLOTS:-24}
22 #if $param_algorithm_max_charge:
23 -algorithm:max_charge $param_algorithm_max_charge
24 #end if
25 #if $param_algorithm_intensity_threshold:
26 -algorithm:intensity_threshold $param_algorithm_intensity_threshold
27 #end if
28 #if $param_algorithm_hr_data:
29 -algorithm:hr_data
30 #end if
18 #if $adv_opts.adv_opts_selector=='advanced': 31 #if $adv_opts.adv_opts_selector=='advanced':
19 -algorithm:intensity_type ${adv_opts.param_intensity_type} 32 #if $adv_opts.param_force:
20 ${adv_opts.param_check_ppm} 33 -force
21 -algorithm:sweep_line:rt_votes_cutoff ${adv_opts.param_rt_votes_cutoff} 34 #end if
22 -algorithm:sweep_line:rt_interleave ${adv_opts.param_rt_interleave} 35 #if $adv_opts.param_algorithm_intensity_type:
36 -algorithm:intensity_type
37 #if &quot; &quot; in str($adv_opts.param_algorithm_intensity_type):
38 &quot;$adv_opts.param_algorithm_intensity_type&quot;
39 #else
40 $adv_opts.param_algorithm_intensity_type
41 #end if
42 #end if
43 #if $adv_opts.param_algorithm_check_ppm:
44 -algorithm:check_ppm
45 #end if
46 #if $adv_opts.param_algorithm_sweep_line_rt_votes_cutoff:
47 -algorithm:sweep_line:rt_votes_cutoff $adv_opts.param_algorithm_sweep_line_rt_votes_cutoff
48 #end if
49 #if $adv_opts.param_algorithm_sweep_line_rt_interleave:
50 -algorithm:sweep_line:rt_interleave $adv_opts.param_algorithm_sweep_line_rt_interleave
51 #end if
23 #end if 52 #end if
24 </command> 53 </command>
25 <inputs> 54 <inputs>
26 <param name="param_in" type="data" format="mzML" optional="False" label="input file" help="(-in)"/> 55 <param format="mzml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
27 <param name="param_max_charge" type="integer" min="1" optional="True" value="3" label="The maximal charge state to be considered." help="(-max_charge)"/> 56 <param help="(-max_charge) " label="The maximal charge state to be considered" min="1" name="param_algorithm_max_charge" optional="True" type="integer" value="3"/>
28 <param name="param_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. If you set intensity_threshold=-1, t' will be zero.#br#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." help="(-intensity_threshold)"/> 57 <param 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" 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" name="param_algorithm_intensity_threshold" type="float" value="-1.0"/>
29 <param name="param_hr_data" type="boolean" truevalue="-algorithm:hr_data true" falsevalue="-algorithm:hr_data false" 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, e.g.). Please check a single MS scan out of your recording, if you are unsure." help="(-hr_data)"/> 58 <param checked="false" falsevalue="" help="(-hr_data) e.g.). Please check a single MS scan out of your recording, if you are unsure" 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," name="param_algorithm_hr_data" optional="True" truevalue="-algorithm:hr_data" type="boolean"/>
30 <expand macro="advanced_options"> 59 <expand macro="advanced_options">
31 <param name="param_intensity_type" type="select" optional="True" value="ref" label="Determines the intensity type returned for the identified features. 'ref' (default) returns the sum of the intensities of each isotopic peak within an isotope pattern. 'trans' refers to the intensity of the monoisotopic peak within the wavelet transform. 'corrected' refers also to the transformed intensity with an attempt to remove the effects of the convolution. While the latter ones might be preferable for qualitative analyses, 'ref' might be the best option to obtain quantitative results. Please note that intensity values might be spoiled (in particular for the option 'ref'), as soon as patterns overlap (see also the explanations given in the class documentation of FeatureFinderAlgorihtmIsotopeWavelet)." help="(-intensity_type)"> 60 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
32 <option value="ref">ref</option> 61 <param help="(-intensity_type) 'ref' (default) returns the sum of the intensities of each isotopic peak within an isotope pattern. 'trans' refers to the intensity of the monoisotopic peak within the wavelet transform. 'corrected' refers also to the transformed intensity with an attempt to remove the effects of the convolution. While the latter ones might be preferable for qualitative analyses, 'ref' might be the best option to obtain quantitative results. Please note that intensity values might be spoiled (in particular for the option 'ref'), as soon as patterns overlap (see also the explanations given in the class documentation of FeatureFinderAlgorihtmIsotopeWavelet)" label="Determines the intensity type returned for the identified features" name="param_algorithm_intensity_type" optional="True" type="select" value="ref">
33 <option value="trans">trans</option> 62 <option value="ref">ref</option>
34 <option value="corrected">corrected</option> 63 <option value="trans">trans</option>
35 </param> 64 <option value="corrected">corrected</option>
36 <param name="param_check_ppm" type="boolean" truevalue="-algorithm:check_ppm true" falsevalue="-algorithm:check_ppm false" checked="false" optional="True" label="Enables/disables a ppm test vs. the averagine model, i.e. potential peptide masses are checked for plausibility. In addition, a heuristic correcting potential mass shifts induced by the wavelet is applied." help="(-check_ppm)"/> 65 </param>
37 <param name="param_rt_votes_cutoff" type="integer" min="0" optional="True" value="5" label="Defines the minimum number of subsequent scans where a pattern must occur to be considered as a feature." help="(-rt_votes_cutoff)"/> 66 <param checked="false" falsevalue="" help="(-check_ppm) the averagine model, i.e. potential peptide masses are checked for plausibility. In addition, a heuristic correcting potential mass shifts induced by the wavelet is applied" label="Enables/disables a ppm test vs" name="param_algorithm_check_ppm" optional="True" truevalue="-algorithm:check_ppm" type="boolean"/>
38 <param name="param_rt_interleave" type="integer" min="0" optional="True" value="1" label="Defines the maximum number of scans (w.r.t. rt_votes_cutoff) where an expected pattern is missing. There is usually no reason to change the default value." help="(-rt_interleave)"/> 67 <param help="(-rt_votes_cutoff) " label="Defines the minimum number of subsequent scans where a pattern must occur to be considered as a feature" min="0" name="param_algorithm_sweep_line_rt_votes_cutoff" optional="True" type="integer" value="5"/>
39 </expand> 68 <param help="(-rt_interleave) rt_votes_cutoff) where an expected pattern is missing. There is usually no reason to change the default value" label="Defines the maximum number of scans (w.r.t" min="0" name="param_algorithm_sweep_line_rt_interleave" optional="True" type="integer" value="1"/>
40 </inputs> 69 </expand>
41 <outputs> 70 </inputs>
42 <data name="param_out" label="output file" format="featureXML"/> 71 <outputs>
43 </outputs> 72 <data format="xml" name="param_out"/>
44 <help>**What it does** 73 </outputs>
45 74 <help>Detects two-dimensional features in LC-MS data.
46 Detects two-dimensional features in LC-MS data.
47 75
48 76
49 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderIsotopeWavelet.html 77 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderIsotopeWavelet.html</help>
50 78 </tool>
51 @REFERENCES@
52 </help>
53 </tool>