Mercurial > repos > galaxyp > msi_combine
comparison msi_combine.xml @ 4:d05bd881af3d draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
author | galaxyp |
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date | Tue, 19 Jun 2018 18:07:04 -0400 |
parents | 91bba2486773 |
children | ff91e78b5c5c |
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3:91bba2486773 | 4:d05bd881af3d |
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1 <tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.1"> | 1 <tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.2"> |
2 <description> | 2 <description> |
3 combine several mass spectrometry imaging datasets into one | 3 combine several mass spectrometry imaging datasets into one |
4 </description> | 4 </description> |
5 <requirements> | 5 <requirements> |
6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> | 6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> |
66 ############## reading files and changing pixel coordinates ################### | 66 ############## reading files and changing pixel coordinates ################### |
67 | 67 |
68 #for $i, $infile in enumerate($infiles): | 68 #for $i, $infile in enumerate($infiles): |
69 | 69 |
70 #if $infile.ext == 'imzml' | 70 #if $infile.ext == 'imzml' |
71 msidata_$i <- readImzML('infile_${i}') | 71 msidata_$i <- readImzML('infile_${i}', mass.accuracy=$accuracy, units.accuracy = "$units") |
72 #elif $infile.ext == 'analyze75' | 72 #elif $infile.ext == 'analyze75' |
73 msidata_$i <- readAnalyze('infile_${i}') | 73 msidata_$i <- readAnalyze('infile_${i}') |
74 #else | 74 #else |
75 msidata_$i = loadRData('infile_${i}.RData') | 75 msidata_$i = loadRData('infile_${i}.RData') |
76 #end if | 76 #end if |
207 coord_fixed()+ | 207 coord_fixed()+ |
208 ggtitle("Spatial orientation of combined data")+ | 208 ggtitle("Spatial orientation of combined data")+ |
209 theme_bw()+ | 209 theme_bw()+ |
210 theme(text=element_text(family="ArialMT", face="bold", size=15))+ | 210 theme(text=element_text(family="ArialMT", face="bold", size=15))+ |
211 theme(legend.position="bottom",legend.direction="vertical")+ | 211 theme(legend.position="bottom",legend.direction="vertical")+ |
212 guides(fill=guide_legend(ncol=4,byrow=TRUE)) | 212 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 6))+ |
213 guides(fill=guide_legend(ncol=5,byrow=TRUE)) | |
213 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean) | 214 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean) |
214 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name) | 215 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name) |
215 for(file_count in 1:nrow(coord_labels)) | 216 for(file_count in 1:nrow(coord_labels)) |
216 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"], | 217 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"], |
217 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))} | 218 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))} |
237 | 238 |
238 ]]></configfile> | 239 ]]></configfile> |
239 </configfiles> | 240 </configfiles> |
240 <inputs> | 241 <inputs> |
241 <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75" | 242 <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75" |
242 label="MSI rawdata as imzml, analyze7.5 or Cardinal MSImageSet saved as RData" | 243 label="MSI data as imzml, analyze7.5 or Cardinal MSImageSet saved as RData" |
243 help="load imzml and ibd file by uploading composite datatype imzml"/> | 244 help="load imzml and ibd file by uploading composite datatype imzml"/> |
245 <param name="accuracy" type="float" value="50" label="Only for processed imzML files: enter 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="units" display="radio" type="select" label="Only for processed imzML files: unit of the mass accuracy" help="either m/z or ppm"> | |
247 <option value="mz" >mz</option> | |
248 <option value="ppm" selected="True" >ppm</option> | |
249 </param> | |
244 <conditional name="combine_conditional"> | 250 <conditional name="combine_conditional"> |
245 <param name="combine_method" type="select" label="Select the way you want to combine multiple files" help="More detailed help can be found in the help section at the bottom"> | 251 <param name="combine_method" type="select" label="Select the way you want to combine multiple files" help="More detailed help can be found in the help section at the bottom"> |
246 <option value="automatic_combine" selected="True" >automatic combination</option> | 252 <option value="automatic_combine" selected="True" >automatic combination</option> |
247 <option value="xy_shifts">xy shifts by hand</option> | 253 <option value="xy_shifts">xy shifts by hand</option> |
248 </param> | 254 </param> |