Mercurial > repos > galaxyp > cardinal_mz_images

comparison macros.xml @ 9:08ebd8da780c draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
author galaxyp
date Thu, 24 Sep 2020 11:35:54 +0000
parents a69865da6f80
children 7828af552085
comparison
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8:a69865da6f80 9:08ebd8da780c
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">
173 173
174 - MSI data: 3 types of input data can be used: 174 - MSI data: 3 types of input data can be used:
175 175
176 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_ 176 - 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) 177 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
178 - Cardinal "MSImageSet" data saved as .RData 178 - Cardinal "MSImageSet" or "MSImagingExperiment" saved as .RData
179 ]]></token> 179 ]]></token>
180 <token name="@MZ_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ 180 <token name="@MZ_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
181 - Optional tabular file with m/z values: 181 - Optional tabular file with m/z values:
182 182
183 - One column with numeric m/z values (without empty fields or letters) 183 - One column with numeric m/z values (without empty fields or letters)
241 <option value="no_processed" selected="True">no</option> 241 <option value="no_processed" selected="True">no</option>
242 <option value="processed">yes</option> 242 <option value="processed">yes</option>
243 </param> 243 </param>
244 <when value="no_processed"/> 244 <when value="no_processed"/>
245 <when value="processed"> 245 <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"/> 246 <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"> 247 <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> 248 <option value="mz" >mz</option>
249 <option value="ppm" selected="True" >ppm</option> 249 <option value="ppm" selected="True" >ppm</option>
250 </param> 250 </param>
251 </when> 251 </when>