Mercurial > repos > recetox > mfassignr_mfassign

comparison macros.xml @ 2:d5745e78fcfe draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit c6e502d8af84750003e4ba001c61817acedd1896
author recetox
date Fri, 13 Sep 2024 10:09:23 +0000
parents 9cbbfd54d7c4
children d2bad53dd220
comparison
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1:9cbbfd54d7c4 2:d5745e78fcfe
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">1.0.3</token> 2 <token name="@TOOL_VERSION@">1.1.1</token>
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="@TOOL_VERSION@">r-mfassignr</requirement> 5 <requirement type="package" version="@TOOL_VERSION@">r-mfassignr</requirement>
6 </requirements> 6 </requirements>
7 </xml> 7 </xml>
94 help= "Lower limit of molecular mass to be assigned."/> 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" 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."/> 96 help= "Upper limit of molecular mass to be assigned."/>
97 </xml> 97 </xml>
98 98
99 <xml name="findrecalseries_param">
100 <param name="input_file" type="data" format="tabular" label="Input data"
101 help= "Recalibration series, output from RecalList"/>
102 <param name="global_min" type="float" label="Global min"
103 help= "A lower bound of the instrument m/z range."/>
104 <param name="global_max" type="float" label="Global max"
105 help= "A higher bound of the instrument m/z range."/>
106 <param name="number_of_combinations" type="integer" label="Number of combinations"
107 help= "Combinations of how many series should be computed." value="5"/>
108 <param name="abundance_score_threshold" type="float" label="Abundance score threshold" value="100"
109 help= "A threshold for filtering abundance score parameter. The series with higher values are better."/>
110 <param name="peak_distance_threshold" type="float" label="Peak distance threshold" value="2"
111 help= "A threshold for the peak distance parameter. The closer this value is to 1, the better."/>
112 <param name="coverage_threshold" type="integer" label="How many % of the m/z range should be covered."
113 help= "How many % of the m/z range should be covered." value="90"/>
114 <param name="fill_series" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Whether to return top 10 unique series (TRUE) or series only from the best combination."
115 help= "If TRUE, top 10 unique series will be returned, otherwise only the series from the best
116 combination will be returned." value="false"/>
117 </xml>
118
99 <xml name="recal_param"> 119 <xml name="recal_param">
100 <param name="input_file" type="data" format="tabular" label="Input data (Output from MFAssign)" 120 <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"/> 121 help= "Input data frame, the output from MFAssign or MFAssignCHO"/>
102 <param name="series" type="data" format="tabular" label="Calibration series (Output from RecalList)" 122 <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."/> 123 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)" 124 <param name="peaks" type="data" format="tabular" label="Peaks dataframe (Mono from IsoFiltR)"
105 help= "Peaks data frame, the Mono output from IsoFiltR"/> 125 help= "Peaks data frame, the Mono output from IsoFiltR"/>
106 <param name="isopeaks" type="data" format="tabular" label="Isopeaks dataframe (Iso from IsoFiltR)" 126 <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"/> 127 help= "Isopeaks data frame, the Mono output from IsoFiltR"/>
108 <expand macro="ionmode_param" /> 128 <expand macro="ionmode_param" />
109 <expand macro="noise_threshold_params" /> 129 <expand macro="noise_threshold_params" />
110 <param name="mzRange" type="float" label="Mass windows used for the segmented recalibration" value="30" 130 <param name="mzRange" type="float" label="Mass windows used for the segmented recalibration" value="30"
111 help= "Mass windows used for the segmented recalibration"/> 131 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" 132 <param name="step_O" type="float" label="Number of oxygen steps for formula extension" value="3"