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comparison preprocessing.xml @ 11:e86a8be551b9 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0c667acd7cc0d0ef6c4e979ca29372b8c0d92c23"
author galaxyp
date Tue, 06 Oct 2020 08:12:49 +0000
parents 5abc3ab4792c
children e0669b1854b1
comparison
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10:5abc3ab4792c 11:e86a8be551b9
1 <tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.0"> 1 <tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.1">
2 <description> 2 <description>
3 mass spectrometry imaging preprocessing 3 mass spectrometry imaging preprocessing
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
334 334
335 #if str( $method.methods_conditional.mz_range.features_filtering) == 'change_mz_range': 335 #if str( $method.methods_conditional.mz_range.features_filtering) == 'change_mz_range':
336 336
337 #if str($processed_cond.processed_file) == "processed": 337 #if str($processed_cond.processed_file) == "processed":
338 338
339 msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, from=$method.methods_conditional.mz_range.min_mz, to=$method.methods_conditional.mz_range.max_mz, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun) 339 msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, from=$method.methods_conditional.mz_range.min_mz, to=$method.methods_conditional.mz_range.max_mz, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun")
340 340
341 #else 341 #else
342 msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun) 342 ## continuous file cannot be binned from m/z to m/z, therefore first cut m/z range and then do mzbin:
343 msidata = msidata[mz(msidata) >= $method.methods_conditional.mz_range.min_mz & mz(msidata) <= $method.methods_conditional.mz_range.max_mz,]
344 msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun")
343 #end if 345 #end if
344 346
345 347
346 #elif str( $method.methods_conditional.mz_range.features_filtering) == 'none': 348 #elif str( $method.methods_conditional.mz_range.features_filtering) == 'none':
347 349