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comparison combine.xml @ 4:48c07268f341 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
author galaxyp
date Fri, 22 Mar 2019 08:18:29 -0400
parents 129cddd02600
children b41107d8fe89
comparison
equal deleted inserted replaced
3:fe5a1d487f32 4:48c07268f341
1 <tool id="cardinal_combine" name="MSI combine" version="@VERSION@.2"> 1 <tool id="cardinal_combine" name="MSI combine" version="@VERSION@.3">
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 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
153 ## shift coordinates according to input tabular file and store file names 153 ## shift coordinates according to input tabular file and store file names
154 coord(msidata_$i)\$x = as.integer(coord(msidata_$i)\$x + input_list[$i+1,$combine_conditional.column_x]) ## shifts x coordinates according to tabular file 154 coord(msidata_$i)\$x = as.integer(coord(msidata_$i)\$x + input_list[$i+1,$combine_conditional.column_x]) ## shifts x coordinates according to tabular file
155 coord(msidata_$i)\$y = as.integer(coord(msidata_$i)\$y + input_list[$i+1,$combine_conditional.column_y]) ## shifts y coordinates according to tabular file 155 coord(msidata_$i)\$y = as.integer(coord(msidata_$i)\$y + input_list[$i+1,$combine_conditional.column_y]) ## shifts y coordinates according to tabular file
156 pixel_vector = append(pixel_vector, rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i))) ## stores file name for each pixel 156 pixel_vector = append(pixel_vector, rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i))) ## stores file name for each pixel
157 msidata_$i\$combined_sample = rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i)) 157 msidata_$i\$combined_sample = rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i))
158 ## store number of file
158 pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i))) 159 pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i)))
159 #silent $pixelcoords.append('pixelcoords_'+str($i)) 160 #silent $pixelcoords.append('pixelcoords_'+str($i))
160 colnames(pixelcoords_$i)[3] = "file_number" 161 colnames(pixelcoords_$i)[3] = "file_number"
161 162
162 ################### preparation automatic combination ########################## 163 ################### preparation automatic combination ##########################
251 count = count +1} 252 count = count +1}
252 253
253 msidata_combined = do.call(combine, datasetlist) 254 msidata_combined = do.call(combine, datasetlist)
254 255
255 msidata = msidata_combined 256 msidata = msidata_combined
257
256 ## save msidata as imzML file 258 ## save msidata as imzML file
257 #if str($imzml_output) == "imzml_format": 259 #if str($imzml_output) == "imzml_format":
258 writeImzML(msidata, "out") 260 writeImzML(msidata, "out")
259 #elif str($imzml_output) == "rdata_format": 261 #elif str($imzml_output) == "rdata_format":
260 ## save as (.RData) 262 ## save as (.RData)
408 410
409 ]]></configfile> 411 ]]></configfile>
410 </configfiles> 412 </configfiles>
411 <inputs> 413 <inputs>
412 <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75" 414 <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75"
413 label="MSI data as imzml, analyze7.5 or Cardinal MSImageSet saved as RData" 415 label="MSI data"
414 help="load imzml and ibd file by uploading composite datatype imzml"/> 416 help="Input file as imzML (composite upload), Analyze7.5 (composite upload) or Cardinal MSImageSet saved as RData (regular upload)"/>
415 <param name="centroids" type="boolean" label="Is the input data centroided (picked)" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/> 417 <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/>
416 <conditional name="processed_cond"> 418 <conditional name="processed_cond">
417 <param name="processed_file" type="select" label="Is the input file a processed imzML file "> 419 <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file">
418 <option value="no_processed" selected="True">not a processed imzML</option> 420 <option value="no_processed" selected="True">no</option>
419 <option value="processed">processed imzML</option> 421 <option value="processed">yes</option>
420 </param> 422 </param>
421 <when value="no_processed"/> 423 <when value="no_processed"/>
422 <when value="processed"> 424 <when value="processed">
423 <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"/> 425 <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"/>
424 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm"> 426 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
455 <param name="xy_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/> 457 <param name="xy_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
456 </when> 458 </when>
457 </conditional> 459 </conditional>
458 <param name="imzml_output" type="select" display = "radio" optional = "False" 460 <param name="imzml_output" type="select" display = "radio" optional = "False"
459 label="Output format" help= "Choose the output format"> 461 label="Output format" help= "Choose the output format">
460 <option value="imzml_format" selected="True">imzML</option> 462 <option value="imzml_format">imzML</option>
461 <option value="rdata_format">RData</option> 463 <option value="rdata_format" selected="True" >RData</option>
462 </param> 464 </param>
463 </inputs> 465 </inputs>
464 <outputs> 466 <outputs>
465 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"> 467 <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML">
466 <filter>imzml_output=='imzml_format'</filter> 468 <filter>imzml_output=='imzml_format'</filter>