Mercurial > repos > galaxyp > msi_preprocessing
comparison msi_preprocessing.xml @ 6:d3fd539f477e draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
author | galaxyp |
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date | Thu, 21 Jun 2018 16:45:55 -0400 |
parents | 2fccfd11360d |
children | 1a3d477bc54a |
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5:2fccfd11360d | 6:d3fd539f477e |
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1 <tool id="mass_spectrometry_imaging_preprocessing" name="MSI preprocessing" version="1.10.0.2"> | 1 <tool id="mass_spectrometry_imaging_preprocessing" name="MSI preprocessing" version="1.10.0.3"> |
2 <description> | 2 <description> |
3 mass spectrometry imaging preprocessing | 3 mass spectrometry imaging preprocessing |
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> |
7 <requirement type="package" version="2.2.1">r-gridextra</requirement> | 7 <requirement type="package" version="2.2.1">r-gridextra</requirement> |
8 <requirement type="package" version="0.20-35">r-lattice</requirement> | 8 <requirement type="package" version="0.20-35">r-lattice</requirement> |
9 <!--requirement type="package" version="3.34.9">bioconductor-limma</requirement--> | |
10 </requirements> | 9 </requirements> |
11 <command detect_errors="exit_code"> | 10 <command detect_errors="exit_code"> |
12 <![CDATA[ | 11 <![CDATA[ |
13 | 12 |
14 #if $infile.ext == 'imzml' | 13 #if $infile.ext == 'imzml' |
32 ################################# load libraries and read file ################# | 31 ################################# load libraries and read file ################# |
33 | 32 |
34 library(Cardinal) | 33 library(Cardinal) |
35 library(gridExtra) | 34 library(gridExtra) |
36 library(lattice) | 35 library(lattice) |
37 ###library(limma) | |
38 | 36 |
39 #if $infile.ext == 'imzml' | 37 #if $infile.ext == 'imzml' |
40 msidata <- readImzML('infile', mass.accuracy=$accuracy, units.accuracy = "$units") | 38 #if str($processed_cond.processed_file) == "processed": |
39 msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units") | |
40 #else | |
41 msidata <- readImzML('infile') | |
42 #end if | |
41 #elif $infile.ext == 'analyze75' | 43 #elif $infile.ext == 'analyze75' |
42 msidata = readAnalyze('infile') | 44 msidata = readAnalyze('infile') |
43 #else | 45 #else |
44 load('infile.RData') | 46 load('infile.RData') |
45 #end if | 47 #end if |
415 </configfiles> | 417 </configfiles> |
416 <inputs> | 418 <inputs> |
417 <param name="infile" type="data" format="imzml,rdata,danalyze75" | 419 <param name="infile" type="data" format="imzml,rdata,danalyze75" |
418 label="MSI data as imzml, analyze7.5 or Cardinal MSImageSet saved as RData" | 420 label="MSI data as imzml, analyze7.5 or Cardinal MSImageSet saved as RData" |
419 help="load imzml and ibd file by uploading composite datatype imzml"/> | 421 help="load imzml and ibd file by uploading composite datatype imzml"/> |
420 <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"/> | 422 <conditional name="processed_cond"> |
421 <param name="units" display="radio" type="select" label="Only for processed imzML files: unit of the mass accuracy" help="either m/z or ppm"> | 423 <param name="processed_file" type="select" label="Is the input file a processed imzML file "> |
422 <option value="mz" >mz</option> | 424 <option value="no_processed" selected="True">not a processed imzML</option> |
423 <option value="ppm" selected="True" >ppm</option> | 425 <option value="processed">processed imzML</option> |
424 </param> | 426 </param> |
427 <when value="no_processed"/> | |
428 <when value="processed"> | |
429 <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"/> | |
430 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm"> | |
431 <option value="mz" >mz</option> | |
432 <option value="ppm" selected="True" >ppm</option> | |
433 </param> | |
434 </when> | |
435 </conditional> | |
425 <repeat name="methods" title="Preprocessing" min="1" max="50"> | 436 <repeat name="methods" title="Preprocessing" min="1" max="50"> |
426 <conditional name="methods_conditional"> | 437 <conditional name="methods_conditional"> |
427 <param name="preprocessing_method" type="select" label="Select the preprocessing methods you want to apply"> | 438 <param name="preprocessing_method" type="select" label="Select the preprocessing methods you want to apply"> |
428 <option value="Normalization" selected="True">Normalization to TIC</option> | 439 <option value="Normalization" selected="True">Normalization to TIC</option> |
429 <option value="Baseline_reduction">Baseline Reduction</option> | 440 <option value="Baseline_reduction">Baseline Reduction</option> |
499 <param name="value_diffalignment" type="integer" value="200" | 510 <param name="value_diffalignment" type="integer" value="200" |
500 label="diff.max" help="Peaks that differ less than this value will be aligned together"/> | 511 label="diff.max" help="Peaks that differ less than this value will be aligned together"/> |
501 <param name="units_diffalignment" type="select" display = "radio" optional = "False" | 512 <param name="units_diffalignment" type="select" display = "radio" optional = "False" |
502 label="units"> | 513 label="units"> |
503 <option value="ppm" selected="True">ppm</option> | 514 <option value="ppm" selected="True">ppm</option> |
504 <option value="Da">Da</option> | 515 <option value="Da">m/z</option> |
505 </param> | 516 </param> |
506 </when> | 517 </when> |
507 <when value="DP"> | 518 <when value="DP"> |
508 <param name="gap_DPalignment" type="integer" value="0" | 519 <param name="gap_DPalignment" type="integer" value="0" |
509 label="Gap" help="The gap penalty for the dynamic programming sequence alignment"/> | 520 label="Gap" help="The gap penalty for the dynamic programming sequence alignment"/> |
788 - Smoothening: Smoothing of the peaks reduces noise and improves peak detection | 799 - Smoothening: Smoothing of the peaks reduces noise and improves peak detection |
789 - Peak picking: relevant peaks are picked while noise-peaks are removed (needs peak alignment afterwards) | 800 - Peak picking: relevant peaks are picked while noise-peaks are removed (needs peak alignment afterwards) |
790 - Peak alignment: only possible after peak picking, m/z inaccuracies are removed by alignment of same peaks to a common m/z value | 801 - Peak alignment: only possible after peak picking, m/z inaccuracies are removed by alignment of same peaks to a common m/z value |
791 - Peak filtering: works only on centroided data (after peak picking and alignment or data reduction with peak filtering), removes peaks that occur only in a small proportion of pixels. If not sure which cutoff to chose run qualitycontrol first and decide according to the zero value plot. | 802 - Peak filtering: works only on centroided data (after peak picking and alignment or data reduction with peak filtering), removes peaks that occur only in a small proportion of pixels. If not sure which cutoff to chose run qualitycontrol first and decide according to the zero value plot. |
792 - Data reduction: binning, resampling or peak filtering to reduce data | 803 - Data reduction: binning, resampling or peak filtering to reduce data |
804 - Transformation: log2 or squareroot transformation of all intensities; when using log2 transformation zero intensities will become NA, this can lead to compatibility problems. | |
793 | 805 |
794 | 806 |
795 Output: | 807 Output: |
796 | 808 |
797 - imzML file, preprocessed | 809 - imzML file, preprocessed |