Mercurial > repos > galaxyp > openms_featurefinderidentification

comparison FeatureFinderIdentification.xml @ 0:3a61c78033f0 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 12:55:55 -0500
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children 6a3bbd5b8cb6
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-1:000000000000 0:3a61c78033f0
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: [Quantitation]-->
4 <tool id="FeatureFinderIdentification" name="FeatureFinderIdentification" version="2.1.0">
5 <description>Detects features in MS1 data based on peptide identifications.</description>
6 <macros>
7 <token name="@EXECUTABLE@">FeatureFinderIdentification</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FeatureFinderIdentification
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_id:
19 -id $param_id
20 #end if
21 #if $param_out:
22 -out $param_out
23 #end if
24 #if $param_lib_out:
25 -lib_out $param_lib_out
26 #end if
27 #if $param_chrom_out:
28 -chrom_out $param_chrom_out
29 #end if
30 #if $param_trafo_out:
31 -trafo_out $param_trafo_out
32 #end if
33 #if $param_extract_reference_rt:
34 -extract:reference_rt $param_extract_reference_rt
35 #end if
36 #if $param_extract_rt_window:
37 -extract:rt_window $param_extract_rt_window
38 #end if
39 #if $param_extract_mz_window:
40 -extract:mz_window $param_extract_mz_window
41 #end if
42 #if $param_extract_isotope_pmin:
43 -extract:isotope_pmin $param_extract_isotope_pmin
44 #end if
45 #if $param_detect_peak_width:
46 -detect:peak_width $param_detect_peak_width
47 #end if
48 #if $param_model_type:
49 -model:type $param_model_type
50 #end if
51 #if $adv_opts.adv_opts_selector=='advanced':
52 #if $adv_opts.param_force:
53 -force
54 #end if
55 #if $adv_opts.param_detect_all_features:
56 -detect:all_features
57 #end if
58 #if $adv_opts.param_model_add_zeros:
59 -model:add_zeros $adv_opts.param_model_add_zeros
60 #end if
61 #if $adv_opts.param_model_unweighted_fit:
62 -model:unweighted_fit
63 #end if
64 #if $adv_opts.param_model_no_imputation:
65 -model:no_imputation
66 #end if
67 #if $adv_opts.param_model_check_boundaries:
68 -model:check:boundaries $adv_opts.param_model_check_boundaries
69 #end if
70 #if $adv_opts.param_model_check_width:
71 -model:check:width $adv_opts.param_model_check_width
72 #end if
73 #if $adv_opts.param_model_check_asymmetry:
74 -model:check:asymmetry $adv_opts.param_model_check_asymmetry
75 #end if
76 #end if
77 </command>
78 <inputs>
79 <param name="param_in" type="data" format="mzml" optional="False" label="Input file (LC-MS raw data)" help="(-in) "/>
80 <param name="param_id" type="data" format="idxml" optional="False" label="Input file (peptide identifications)" help="(-id) "/>
81 <param name="param_extract_reference_rt" type="select" optional="False" value="adapt" label="Method for selecting the reference RT, if there are multiple IDs for a peptide and charge" help="(-reference_rt) 'adapt': adapt (extend) RT windows based on IDs; 'score': RT of the best-scoring ID; 'intensity': RT of the ID with the most intense precursor; 'median': median RT of all IDs; 'all': no single reference, use RTs of all IDs (requires further processing of results)">
82 <option value="adapt" selected="true">adapt</option>
83 <option value="score">score</option>
84 <option value="intensity">intensity</option>
85 <option value="median">median</option>
86 <option value="all">all</option>
87 </param>
88 <param name="param_extract_rt_window" type="float" min="0.0" optional="True" value="60.0" label="RT window size (in sec.) for chromatogram extraction" help="(-rt_window) "/>
89 <param name="param_extract_mz_window" type="float" min="0.0" optional="True" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help="(-mz_window) "/>
90 <param name="param_extract_isotope_pmin" type="float" min="0.0" max="1.0" optional="True" value="0.03" label="Minimum probability for an isotope to be included in the assay for a peptide" help="(-isotope_pmin) "/>
91 <param name="param_detect_peak_width" type="float" min="0.0" optional="True" value="30.0" label="Elution peak width in seconds for smoothing (Gauss filter)" help="(-peak_width) "/>
92 <param name="param_model_type" display="radio" type="select" optional="False" value="symmetric" label="Type of elution model to fit to features" help="(-type) ">
93 <option value="symmetric" selected="true">symmetric</option>
94 <option value="asymmetric">asymmetric</option>
95 <option value="none">none</option>
96 </param>
97 <expand macro="advanced_options">
98 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
99 <param name="param_detect_all_features" display="radio" type="boolean" truevalue="-detect:all_features" falsevalue="" checked="false" optional="True" label="Return all features detected by OpenSWATH for an assay, instead of only the best one" help="(-all_features) (This requires further processing of the results.)"/>
100 <param name="param_model_add_zeros" type="float" min="0.0" optional="True" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="(-add_zeros) This parameter sets the weight given to these points during model fitting; '0' to disable"/>
101 <param name="param_model_unweighted_fit" display="radio" type="boolean" truevalue="-model:unweighted_fit" falsevalue="" checked="false" optional="True" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help="(-unweighted_fit) "/>
102 <param name="param_model_no_imputation" display="radio" type="boolean" truevalue="-model:no_imputation" falsevalue="" checked="false" optional="True" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help="(-no_imputation) "/>
103 <param name="param_model_check_boundaries" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help="(-boundaries) "/>
104 <param name="param_model_check_width" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores; '0' to disable" help="(-width) "/>
105 <param name="param_model_check_asymmetry" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable" help="(-asymmetry) "/>
106 </expand>
107 </inputs>
108 <outputs>
109 <data name="param_out" format="featurexml"/>
110 <data name="param_lib_out" format="traml"/>
111 <data name="param_chrom_out" format="mzml"/>
112 <data name="param_trafo_out" format="trafoxml"/>
113 </outputs>
114 <help>Detects features in MS1 data based on peptide identifications.
115
116
117 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderIdentification.html</help>
118 </tool>