annotate macros.xml @ 0:6e1813883a9a draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
author recetox
date Thu, 15 Aug 2024 12:00:39 +0000 (4 months ago)
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children 7e5ccc8b6f6e
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6e1813883a9a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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1 <macros>
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2 <token name="@TOOL_VERSION@">1.0.3</token>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="@TOOL_VERSION@">r-mfassignr</requirement>
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6 </requirements>
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7 </xml>
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8
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9 <xml name="refs">
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10 <xrefs>
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11 <xref type="bio.tools">mfassignr</xref>
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12 </xrefs>
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13 </xml>
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14
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15 <xml name="creator">
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16 <creator>
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17 <person
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18 givenName="Kristina"
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19 familyName="Gomoryova"
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20 url="https://github.com/KristinaGomoryova"
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21 identifier="0000-0003-4407-3917" />
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22 <person
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23 givenName="Helge"
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24 familyName="Hecht"
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25 url="https://github.com/hechth"
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26 identifier="0000-0001-6744-996X" />
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27 <person
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28 givenName="Zargham"
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29 familyName="Ahmad"
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30 url="https://github.com/zargham-ahmad"
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31 identifier="0000-0002-6096-224X" />
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32 <organization
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33 url="https://www.recetox.muni.cz/"
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34 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
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35 name="RECETOX MUNI" />
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36 </creator>
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37 </xml>
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38
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39 <xml name="kmdnoise_param">
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40 <param name="input_file" type="data" format="tabular" label="Input data"
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41 help= "Input data frame, first column is mass, second column is intensity"/>
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42 <param name="upper_y" type="float" label="upper limit for the y intercept" value="0.2"
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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."/>
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44 <param name="lower_y" type="float" label="lower limit for the y intercept" value="0.05"
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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."/>
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46 <param name="upper_x" optional="true" type="float" label="upper limit for the x intercept"
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47 help="If not set, it defaults to maximum mass in the mass spectrum."/>
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48 <param name="lower_x" optional="true" type="float" label="lower limit for the x intercept"
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49 help="If not set, it defaults to minimum mass in the mass spectrum."/>
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50 </xml>
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51
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52 <xml name="histnoise_param">
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53 <param name="input_file" type="data" format="tabular" label="Input data"
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54 help= "Input data frame, first column is mass, second column is intensity"/>
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55 <param name="SN" type="float" label="signal-to-noise threshold" value="0"
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56 help= "A numeric value for situations where a predefined noise value is desired, default is 0"/>
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57 <param name="bin" type="float" label="bindwidth of the histogram" value="0.01"
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58 help= "A numeric value determining the binwidth of the histogram, default is 0.01"/>
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59 </xml>
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60
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61 <xml name="noise_threshold_params">
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62 <param name="sn_ratio" type="float" label="SN ratio" value="6"
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63 help= "Noise multiplier. Recommended value is 6."/>
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64 <param name="kmdn" type="float" label="Estimated noise" value="0"
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65 help= "Estimated noise, either from the KMDNoise or HistNoise function."/>
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66 </xml>
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67
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68 <xml name="snplot_param">
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69 <param name="input_file" type="data" format="tabular" label="Input data"
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70 help= "Input data frame, first column is mass, second column is intensity"/>
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71 <param name="cut" type="float" label="cut"
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72 help= "A numeric value of the intensity cut value being investigated"/>
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73 <param name="mass" type="float" label="mass"
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74 help= "A numeric value setting a centerpoint to look at the mass spectrum"/>
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75 <param name="window_x" type="float" label="window.x" value="0.5"
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76 help= "A numeric value setting the +/- range around the mass centerpoint, default is 0.5"/>
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77 <param name="window_y" type="float" label="window.y" value="10"
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78 help= "A numeric value setting the y axis value for the plot, determined by multiplying the cut by this value"/>
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79 </xml>
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80
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81 <xml name="ionmode_param">
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82 <param name="ionmode" type="select" display="radio" label="Ion mode" help= "The ionization mode.">
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83 <option value="neg" >negative</option>
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84 <option value="pos" selected="true">positive</option>
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85 </param>
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86 </xml>
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87
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88 <xml name="mfassign_param">
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89 <param name="ppm_err" type="integer" label="ppm_err"
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90 help= "Error tolerance (ppm) for formula assignment" value="3"/>
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91 <expand macro="ionmode_param" />
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92 <expand macro="noise_threshold_params" />
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93 <param name="lowMW" type="float" label="Lower limit of molecular mass to be assigned" value="100"
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94 help= "Lower limit of molecular mass to be assigned."/>
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95 <param name="highMW" type="float" label="Upper limit of molecular mass to be assigned" value="1000"
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96 help= "Upper limit of molecular mass to be assigned."/>
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97 </xml>
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98
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99 <xml name="recal_param">
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100 <param name="input_file" type="data" format="tabular" label="Input data (Output from MFAssign)"
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101 help= "Input data frame, the output from MFAssign or MFAssignCHO"/>
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102 <param name="series" type="data" format="tabular" label="Calibration series (Output from RecalList)"
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103 help= "Calibration series (Output from RecalList). At maximum the first 10 rows are used."/>
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104 <param name="peaks" type="data" format="tabular" label="Peaks dataframe (Mono from IsoFiltR)"
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105 help= "Peaks data frame, the Mono output from IsoFiltR"/>
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106 <param name="isopeaks" type="data" format="tabular" label="Isopeaks dataframe (Iso from IsoFiltR)"
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107 optional="true" help= "Isopeaks data frame, the Mono output from IsoFiltR"/>
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108 <expand macro="ionmode_param" />
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109 <expand macro="noise_threshold_params" />
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110 <param name="mzRange" type="float" label="Mass windows used for the segmented recalibration" value="30"
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111 help= "Mass windows used for the segmented recalibration"/>
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112 <param name="step_O" type="float" label="Number of oxygen steps for formula extension" value="3"
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113 help= "Number of oxygen steps for formula extension"/>
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114 <param name="step_H2" type="float" label="Number of H2 steps for formula extension" value="5"
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115 help= "Number of H2 steps for formula extension"/>
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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"/>
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117
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118 </xml>
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119
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120 <xml name="isofiltr_param">
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121 <param name="peaks" type="data" format="tabular" label="Input Peak Data"
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122 help="The input data frame containing abundance and peak mass."/>
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123 <param name="SN" type="float" value="0" label="Signal-to-Noise Ratio"
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124 help="Sets the noise cut for the data; peaks below this value will not be evaluated."/>
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125 <param name="Carbrat" type="float" value="60" min="5" label="Maximum 13C/12C Ratio"
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126 help="Sets the maximum allowed ratio for matching 13C isotopes."/>
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127 <param name="Sulfrat" type="float" value="30" label="Maximum 34S/32S Ratio"
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128 help="Sets the maximum allowed ratio for matching 34S isotopes."/>
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129 <param name="Sulferr" type="float" value="5" label="Maximum Error for 34S Matching (ppm)"
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130 help="Sets the maximum allowed error (ppm) for 34S mass matching."/>
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131 <param name="Carberr" type="float" value="5" label="Maximum Error for 13C Matching (ppm)"
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132 help="Sets the maximum allowed error (ppm) for 13C mass matching."/>
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133 </xml>
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134
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135 <xml name="citations">
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136 <citations>
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137 <citation type="doi">10.1016/j.envres.2020.110114</citation>
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138 </citations>
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139 </xml>
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140
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141 </macros>