Mercurial > repos > computational-metabolomics > dimspy_process_scans

comparison process_scans.xml @ 1:deafa30d6570 draft

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"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 680116d0cf6a6d7246cba655452dea43269aeba4"
author computational-metabolomics
date Tue, 28 Apr 2020 17:32:59 -0400
parents 62c4813fbe7a
children bc099f2346a1
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0:62c4813fbe7a 1:deafa30d6570
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
8 <![CDATA[ 8 <![CDATA[
9 #if $data.input[0].is_of_type("zip") 9 #if $data.input[0].is_of_type("zip")
10 dimspy unzip
11 --input $data.input[0]
12 --output ./data
13 &&
10 dimspy process-scans 14 dimspy process-scans
11 --input $data.input[0] 15 --input ./data
12 #else 16 #else
13 #for $fn in $data.input 17 #for $fn in $data.input
14 ln -s '$fn' '$fn.name' 18 ln -s '$fn' '$fn.name'
15 && 19 &&
16 #end for 20 #end for
210 ---------------- 214 ----------------
211 215
212 Description 216 Description
213 ----------- 217 -----------
214 218
215 Standard DIMS processing workflow: **Process Scans** -> Replicate Filter -> Align Samples -> [Missing values sample filter] -> Blank Filter -> Sample Filter -> Matrix processing -> Statistics 219 Standard DIMS processing workflow: **Process Scans** -> [Replicate Filter] -> Align Samples -> [Missing values sample filter] -> Blank Filter -> Sample Filter -> [Missing values sample filter] -> Pre-processing -> Statistics
216 220
217 This tool is used to generate a single mass spectral peaklist for each of the data files defined in the ‘Filelist/Samplelist’. The tool extracts mass spectral peaks from a data file (in either .mzML or .RAW format) and then filters these in accordance with user-defined parameter settings. All peaks remaining after filtering are hierarchically clustered in one-dimension, during which pairs of peaks with similar m/z values are grouped together if the difference between their m/z values, when divided by the average of their m/z values and multiplied by 1 x 10\ :sup:`6` \, equates to less-than the user-defined ppm error tolerance. 221 This tool is used to generate a single mass spectral peaklist for each of the data files defined in the ‘Filelist/Samplelist’. The tool extracts mass spectral peaks from a data file (in either .mzML or .RAW format) and then filters these in accordance with user-defined parameter settings. All peaks remaining after filtering are hierarchically clustered in one-dimension, during which pairs of peaks with similar m/z values are grouped together if the difference between their m/z values, when divided by the average of their m/z values and multiplied by 1 x 10\ :sup:`6` \, equates to less-than the user-defined ppm error tolerance.
218 222
219 **IMPORTANT:** when using .mzML files generated using the Proteowizard tool, SIM-type scans will only be treated as spectra if the ‘simAsSpectra’ filter was set to true during the conversion process, e.g.: 223 **IMPORTANT:** when using .mzML files generated using the Proteowizard tool, SIM-type scans will only be treated as spectra if the ‘simAsSpectra’ filter was set to true during the conversion process, e.g.:
220 224