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comparison macros.xml @ 9:e0bbaf9f7da0 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
author galaxyp
date Tue, 03 Nov 2020 22:41:21 +0000
parents 413a1b74f496
children aa479a0cfb43
comparison
equal deleted inserted replaced
8:413a1b74f496 9:e0bbaf9f7da0
1 <macros> 1 <macros>
2 <token name="@VERSION@">2.4.0</token> 2 <token name="@VERSION@">2.6.0</token>
3 3
4 <xml name="requirements"> 4 <xml name="requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement> 6 <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement>
7 <requirement type="package" version="3.6.1">r-base</requirement> 7 <!--requirement type="package" version="3.6.1">r-base</requirement-->
8 <yield/> 8 <yield/>
9 </requirements> 9 </requirements>
10 </xml> 10 </xml>
11 11
12 <xml name="print_version"> 12 <xml name="print_version">
115 ]]></token> 115 ]]></token>
116 116
117 <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[ 117 <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[
118 ########################### QC numbers ######################## 118 ########################### QC numbers ########################
119 ## including intensity calculations which need data in RAM 119 ## including intensity calculations which need data in RAM
120
121 int_matrix = as.matrix(spectra(msidata)) ## only load once into RAM, then re-use
122 ## Number of NA in spectra matrix
123 NAcount = sum(is.na(int_matrix))
124 ## replace NA with zero to calculate data properties based on intensity matrix, no change in msidata
125 int_matrix[is.na(int_matrix)] <- 0
126
120 ## Number of features (mz) 127 ## Number of features (mz)
121 maxfeatures = length(features(msidata)) 128 maxfeatures = length(features(msidata))
122 ## Range mz 129 ## Range mz
123 minmz = round(min(mz(msidata)), digits=2) 130 minmz = round(min(mz(msidata)), digits=2)
124 maxmz = round(max(mz(msidata)), digits=2) 131 maxmz = round(max(mz(msidata)), digits=2)
129 maximumx = max(coord(msidata)[,1]) 136 maximumx = max(coord(msidata)[,1])
130 ## Range y coordinates 137 ## Range y coordinates
131 minimumy = min(coord(msidata)[,2]) 138 minimumy = min(coord(msidata)[,2])
132 maximumy = max(coord(msidata)[,2]) 139 maximumy = max(coord(msidata)[,2])
133 ## Range of intensities 140 ## Range of intensities
134 minint = round(min(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2) 141 minint = round(min(int_matrix), digits=2)
135 maxint = round(max(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2) 142 maxint = round(max(int_matrix), digits=2)
136 ## Number of intensities > 0, for if conditions 143 ## Number of intensities > 0, for if conditions
137 npeaks= sum(as.matrix(spectra(msidata))>0, na.rm=TRUE) 144 npeaks= sum(int_matrix>0)
138 ## Number of NA in spectra matrix 145 ## Number of NA in spectra matrix
139 NAcount = sum(is.na(spectra(msidata))) 146 infcount = sum(is.infinite(int_matrix))
140 ## Number of NA in spectra matrix
141 infcount = sum(is.infinite(as.matrix(spectra(msidata))))
142 ## Number of duplicated coordinates 147 ## Number of duplicated coordinates
143 dupl_coord = sum(duplicated(coord(msidata))) 148 dupl_coord = sum(duplicated(coord(msidata)))
144 properties = c("Number of m/z features", 149 properties = c("Number of m/z features",
145 "Range of m/z values", 150 "Range of m/z values",
146 "Number of pixels", 151 "Number of pixels",
173 178
174 - MSI data: 3 types of input data can be used: 179 - MSI data: 3 types of input data can be used:
175 180
176 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_ 181 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
177 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function) 182 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
178 - Cardinal "MSImageSet" data saved as .RData 183 - Cardinal "MSImageSet" or "MSImagingExperiment" saved as .RData
179 ]]></token> 184 ]]></token>
180 <token name="@MZ_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ 185 <token name="@MZ_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
181 - Optional tabular file with m/z values: 186 - Optional tabular file with m/z values:
182 187
183 - One column with numeric m/z values (without empty fields or letters) 188 - One column with numeric m/z values (without empty fields or letters)
241 <option value="no_processed" selected="True">no</option> 246 <option value="no_processed" selected="True">no</option>
242 <option value="processed">yes</option> 247 <option value="processed">yes</option>
243 </param> 248 </param>
244 <when value="no_processed"/> 249 <when value="no_processed"/>
245 <when value="processed"> 250 <when value="processed">
246 <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/> 251 <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned"/>
247 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm"> 252 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
248 <option value="mz" >mz</option> 253 <option value="mz" >mz</option>
249 <option value="ppm" selected="True" >ppm</option> 254 <option value="ppm" selected="True" >ppm</option>
250 </param> 255 </param>
251 </when> 256 </when>