Mercurial > repos > galaxyp > cardinal_preprocessing

comparison macros.xml @ 11:3161cb3810c0 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
author galaxyp
date Tue, 22 Feb 2022 20:37:33 +0000
parents aa479a0cfb43
children a9b90620b7a4
comparison
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10:aa479a0cfb43 11:3161cb3810c0
176 <token name="@MSIDATA_INPUT_DESCRIPTION@"><![CDATA[ 176 <token name="@MSIDATA_INPUT_DESCRIPTION@"><![CDATA[
177 **Input data** 177 **Input data**
178 178
179 - MSI data: 3 types of input data can be used: 179 - MSI data: 3 types of input data can be used:
180 180
181 - 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/imzml/>`_
182 - 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)
183 - Cardinal "MSImageSet" or "MSImagingExperiment" saved as .RData 183 - Cardinal "MSImageSet" or "MSImagingExperiment" saved as .RData
184 ]]></token> 184 ]]></token>
185 <token name="@MZ_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ 185 <token name="@MZ_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
186 - Optional tabular file with m/z values: 186 - Optional tabular file with m/z values:
217 ... 217 ...
218 ... 218 ...
219 219
220 ]]></token> 220 ]]></token>
221 <token name="@SPECTRA_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ 221 <token name="@SPECTRA_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
222 - Optional file with pixel coordinates and annotation: 222 - Optional file with pixel coordinates and annotation:
223 223
224 - Tabular file: One column with x values, one column with y values and one column with annotations 224 - Tabular file: One column with x values, one column with y values and one column with annotations
225 - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes) 225 - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
226 - Pixel with coordinates outside the coordinates of the input file are ignored 226 - Pixel with coordinates outside the coordinates of the input file are ignored
227 227
228
228 :: 229 ::
229 230
230 x_coord y_coord annotation 231 x_coord y_coord annotation
231 1 1 healthy 232 1 1 healthy
232 2 1 healthy 233 2 1 healthy
233 3 1 disease 234 3 1 disease
234 ... 235 ...
235 ... 236 ...
236
237 ]]></token> 237 ]]></token>
238 238
239 <xml name="reading_msidata"> 239 <xml name="reading_msidata">
240 <param name="infile" type="data" format="imzml,rdata,analyze75" 240 <param name="infile" type="data" format="imzml,rdata,analyze75"
241 label="MSI data" 241 label="MSI data"