Mercurial > repos > recetox > mfassignr_kmdnoise

comparison macros.xml @ 0:f60df05dd038 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
author recetox
date Thu, 15 Aug 2024 12:02:14 +0000
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children 99d021734000
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-1:000000000000 0:f60df05dd038
1 <macros>
2 <token name="@TOOL_VERSION@">1.0.3</token>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="@TOOL_VERSION@">r-mfassignr</requirement>
6 </requirements>
7 </xml>
8
9 <xml name="refs">
10 <xrefs>
11 <xref type="bio.tools">mfassignr</xref>
12 </xrefs>
13 </xml>
14
15 <xml name="creator">
16 <creator>
17 <person
18 givenName="Kristina"
19 familyName="Gomoryova"
20 url="https://github.com/KristinaGomoryova"
21 identifier="0000-0003-4407-3917" />
22 <person
23 givenName="Helge"
24 familyName="Hecht"
25 url="https://github.com/hechth"
26 identifier="0000-0001-6744-996X" />
27 <person
28 givenName="Zargham"
29 familyName="Ahmad"
30 url="https://github.com/zargham-ahmad"
31 identifier="0000-0002-6096-224X" />
32 <organization
33 url="https://www.recetox.muni.cz/"
34 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
35 name="RECETOX MUNI" />
36 </creator>
37 </xml>
38
39 <xml name="kmdnoise_param">
40 <param name="input_file" type="data" format="tabular" label="Input data"
41 help= "Input data frame, first column is mass, second column is intensity"/>
42 <param name="upper_y" type="float" label="upper limit for the y intercept" value="0.2"
43 help= "The upper y-intercept value to isolate noise peaks in the equation for the KMD plot: y = 0.001123*x + b. Default value is set to 0.2, so that it does not interact with any potentially double-charged peaks."/>
44 <param name="lower_y" type="float" label="lower limit for the y intercept" value="0.05"
45 help="The lower y-intercept value to isolate noise peaks in the equation for the KMD plot: y = 0.001123*x + b. Default value is set to 0.05 to ensure no analyte peaks are incorporated into the noise estimation."/>
46 <param name="upper_x" optional="true" type="float" label="upper limit for the x intercept"
47 help="If not set, it defaults to maximum mass in the mass spectrum."/>
48 <param name="lower_x" optional="true" type="float" label="lower limit for the x intercept"
49 help="If not set, it defaults to minimum mass in the mass spectrum."/>
50 </xml>
51
52 <xml name="histnoise_param">
53 <param name="input_file" type="data" format="tabular" label="Input data"
54 help= "Input data frame, first column is mass, second column is intensity"/>
55 <param name="SN" type="float" label="signal-to-noise threshold" value="0"
56 help= "A numeric value for situations where a predefined noise value is desired, default is 0"/>
57 <param name="bin" type="float" label="bindwidth of the histogram" value="0.01"
58 help= "A numeric value determining the binwidth of the histogram, default is 0.01"/>
59 </xml>
60
61 <xml name="noise_threshold_params">
62 <param name="sn_ratio" type="float" label="SN ratio" value="6"
63 help= "Noise multiplier. Recommended value is 6."/>
64 <param name="kmdn" type="float" label="Estimated noise" value="0"
65 help= "Estimated noise, either from the KMDNoise or HistNoise function."/>
66 </xml>
67
68 <xml name="snplot_param">
69 <param name="input_file" type="data" format="tabular" label="Input data"
70 help= "Input data frame, first column is mass, second column is intensity"/>
71 <param name="cut" type="float" label="cut"
72 help= "A numeric value of the intensity cut value being investigated"/>
73 <param name="mass" type="float" label="mass"
74 help= "A numeric value setting a centerpoint to look at the mass spectrum"/>
75 <param name="window_x" type="float" label="window.x" value="0.5"
76 help= "A numeric value setting the +/- range around the mass centerpoint, default is 0.5"/>
77 <param name="window_y" type="float" label="window.y" value="10"
78 help= "A numeric value setting the y axis value for the plot, determined by multiplying the cut by this value"/>
79 </xml>
80
81 <xml name="ionmode_param">
82 <param name="ionmode" type="select" display="radio" label="Ion mode" help= "The ionization mode.">
83 <option value="neg" >negative</option>
84 <option value="pos" selected="true">positive</option>
85 </param>
86 </xml>
87
88 <xml name="mfassign_param">
89 <param name="ppm_err" type="integer" label="ppm_err"
90 help= "Error tolerance (ppm) for formula assignment" value="3"/>
91 <expand macro="ionmode_param" />
92 <expand macro="noise_threshold_params" />
93 <param name="lowMW" type="float" label="Lower limit of molecular mass to be assigned" value="100"
94 help= "Lower limit of molecular mass to be assigned."/>
95 <param name="highMW" type="float" label="Upper limit of molecular mass to be assigned" value="1000"
96 help= "Upper limit of molecular mass to be assigned."/>
97 </xml>
98
99 <xml name="recal_param">
100 <param name="input_file" type="data" format="tabular" label="Input data (Output from MFAssign)"
101 help= "Input data frame, the output from MFAssign or MFAssignCHO"/>
102 <param name="series" type="data" format="tabular" label="Calibration series (Output from RecalList)"
103 help= "Calibration series (Output from RecalList). At maximum the first 10 rows are used."/>
104 <param name="peaks" type="data" format="tabular" label="Peaks dataframe (Mono from IsoFiltR)"
105 help= "Peaks data frame, the Mono output from IsoFiltR"/>
106 <param name="isopeaks" type="data" format="tabular" label="Isopeaks dataframe (Iso from IsoFiltR)"
107 optional="true" help= "Isopeaks data frame, the Mono output from IsoFiltR"/>
108 <expand macro="ionmode_param" />
109 <expand macro="noise_threshold_params" />
110 <param name="mzRange" type="float" label="Mass windows used for the segmented recalibration" value="30"
111 help= "Mass windows used for the segmented recalibration"/>
112 <param name="step_O" type="float" label="Number of oxygen steps for formula extension" value="3"
113 help= "Number of oxygen steps for formula extension"/>
114 <param name="step_H2" type="float" label="Number of H2 steps for formula extension" value="5"
115 help= "Number of H2 steps for formula extension"/>
116 <param name="CalPeak" type="float" label="Maximum allowed recalibrant peaks per mzRange defined segment" value="150" help= "Maximum allowed recalibrant peaks per mzRange defined segment"/>
117
118 </xml>
119
120 <xml name="isofiltr_param">
121 <param name="peaks" type="data" format="tabular" label="Input Peak Data"
122 help="The input data frame containing abundance and peak mass."/>
123 <param name="SN" type="float" value="0" label="Signal-to-Noise Ratio"
124 help="Sets the noise cut for the data; peaks below this value will not be evaluated."/>
125 <param name="Carbrat" type="float" value="60" min="5" label="Maximum 13C/12C Ratio"
126 help="Sets the maximum allowed ratio for matching 13C isotopes."/>
127 <param name="Sulfrat" type="float" value="30" label="Maximum 34S/32S Ratio"
128 help="Sets the maximum allowed ratio for matching 34S isotopes."/>
129 <param name="Sulferr" type="float" value="5" label="Maximum Error for 34S Matching (ppm)"
130 help="Sets the maximum allowed error (ppm) for 34S mass matching."/>
131 <param name="Carberr" type="float" value="5" label="Maximum Error for 13C Matching (ppm)"
132 help="Sets the maximum allowed error (ppm) for 13C mass matching."/>
133 </xml>
134
135 <xml name="citations">
136 <citations>
137 <citation type="doi">10.1016/j.envres.2020.110114</citation>
138 </citations>
139 </xml>
140
141 </macros>