Mercurial > repos > galaxyp > msi_filtering

annotate msi_filtering.xml @ 1:98c101b19f3c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
author galaxyp
date Mon, 23 Apr 2018 17:18:35 -0400
parents f17d3f1a065f
children 22db5eb94e50
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
1 <tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.7.0.1">
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
2 <description>tool for filtering mass spectrometry imaging data</description>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
3 <requirements>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
4 <requirement type="package" version="1.7.0">bioconductor-cardinal</requirement>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
5 <requirement type="package" version="2.2.1">r-gridextra</requirement>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
6 </requirements>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
7 <command detect_errors="exit_code">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
8 <![CDATA[
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
9
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
10 #if $infile.ext == 'imzml'
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
11 cp '${infile.extra_files_path}/imzml' infile.imzML &&
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
12 cp '${infile.extra_files_path}/ibd' infile.ibd &&
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
13 #elif $infile.ext == 'analyze75'
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
14 cp '${infile.extra_files_path}/hdr' infile.hdr &&
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
15 cp '${infile.extra_files_path}/img' infile.img &&
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
16 cp '${infile.extra_files_path}/t2m' infile.t2m &&
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
17 #else
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
18 ln -s $infile infile.RData &&
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
19 #end if
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
20 cat '${MSI_subsetting}' &&
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
21 echo ${MSI_subsetting} &&
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
22 Rscript '${MSI_subsetting}'
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
23
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
24 ]]>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
25 </command>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
26 <configfiles>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
27 <configfile name="MSI_subsetting"><![CDATA[
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
28
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
29
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
30 ################################# load libraries and read file #########################
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
31
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
32
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
33 library(Cardinal)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
34 library(gridExtra)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
35
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
36 ## Read MALDI Imaging dataset
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
37
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
38 #if $infile.ext == 'imzml'
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
39 msidata = readMSIData('infile.imzML')
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
40 #elif $infile.ext == 'analyze75'
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
41 msidata = readMSIData('infile.hdr')
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
42 #else
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
43 load('infile.RData')
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
44 #end if
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
45
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
46 ###################################### inputfile properties in numbers ######################
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
47
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
48 #if $outputs.outputs_select == "quality_control":
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
49 ## Number of features (mz)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
50 maxfeatures = length(features(msidata))
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
51 ## Range mz
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
52 minmz = round(min(mz(msidata)), digits=2)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
53 maxmz = round(max(mz(msidata)), digits=2)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
54 ## Number of spectra (pixels)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
55 pixelcount = length(pixels(msidata))
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
56 ## Range x coordinates
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
57 minimumx = min(coord(msidata)[,1])
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
58 maximumx = max(coord(msidata)[,1])
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
59 ## Range y coordinates
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
60 minimumy = min(coord(msidata)[,2])
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
61 maximumy = max(coord(msidata)[,2])
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
62 ## Number of intensities > 0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
63 npeaks= sum(spectra(msidata)[]>0)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
64 ## Spectra multiplied with mz (potential number of peaks)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
65 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
66 ## Percentage of intensities > 0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
67 percpeaks = round(npeaks/numpeaks*100, digits=2)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
68 ## Number of empty TICs
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
69 TICs = colSums(spectra(msidata)[])
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
70 NumemptyTIC = sum(TICs == 0)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
71 ## median TIC
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
72 medint = round(median(TICs), digits=2)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
73 ## Store features for QC plot
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
74 featuresinfile = mz(msidata)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
75 #end if
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
76
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
77
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
78 ###################################### filtering of pixels ######################
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
79
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
80 #if str($pixels_cond.pixel_filtering) == "single_column":
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
81 print("single column")
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
82
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
83 #if $pixels_cond.single_pixels:
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
84 input_list = read.delim("$pixels_cond.single_pixels", header = FALSE, stringsAsFactors = FALSE)
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
85 numberpixels = length(input_list[,$pixels_cond.pixel_column])
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
86 valid_entries = input_list[,$pixels_cond.pixel_column] %in% names(pixels(msidata))
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
87 validpixels = sum(valid_entries)
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
88
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
89 if (validpixels != 0)
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
90 {
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
91 pixelsofinterest = pixels(msidata)[names(pixels(msidata)) %in% input_list[valid_entries,$pixels_cond.pixel_column]]
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
92 msidata = msidata[,pixelsofinterest]
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
93 }else{
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
94 validpixels=0
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
95 }
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
96
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
97 #else
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
98 validpixels=0
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
99 numberpixels = 0
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
100 #end if
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
101
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
102 #elif str($pixels_cond.pixel_filtering) == "two_columns":
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
103 print("two columns")
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
104
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
105 #if $pixels_cond.two_columns_pixel:
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
106
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
107 input_list = read.delim("$pixels_cond.two_columns_pixel", header = FALSE,
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
108 stringsAsFactors = FALSE)
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
109 numberpixels = length(input_list[,$pixels_cond.pixel_column_x])
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
110
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
111 inputpixel_x = input_list[,$pixels_cond.pixel_column_x]
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
112 inputpixel_y = input_list[,$pixels_cond.pixel_column_y]
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
113
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
114 inputpixels = cbind(inputpixel_x, inputpixel_y)
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
115 colnames(inputpixels) = c("x", "y")
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
116 valid_rows = merge(inputpixels, coord(msidata)[,1:2])
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
117 validpixels = nrow(valid_rows)
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
118
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
119 if (validpixels != 0)
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
120 {
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
121
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
122 pixelvector = character()
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
123
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
124 for (pixel in 1:nrow(valid_rows))
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
125 {
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
126 pixelvector[pixel] = paste0("x = ", valid_rows[pixel,1],", ", "y = ", valid_rows[pixel,2])
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
127 }
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
128
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
129 pixelsofinterest= pixels(msidata)[names(pixels(msidata)) %in% pixelvector]
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
130 msidata = msidata[,pixelsofinterest]
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
131 }else{
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
132 validpixels=0
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
133 }
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
134
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
135
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
136 #else
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
137 validpixels=0
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
138 numberpixels = 0
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
139 #end if
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
140
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
141 #elif str($pixels_cond.pixel_filtering) == "pixel_range":
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
142 print("pixel range")
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
143
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
144 numberpixels = "range"
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
145 validpixels = "range"
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
146
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
147 if (sum(coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range) > 0)
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
148 {
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
149 msidata = msidata[, coord(msidata)\$x <= $pixels_cond.max_x_range & coord(msidata)\$x >= $pixels_cond.min_x_range]
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
150 }
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
151
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
152 if (sum(coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range) > 0)
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
153 {
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
154 msidata = msidata[, coord(msidata)\$y <= $pixels_cond.max_y_range & coord(msidata)\$y >= $pixels_cond.min_y_range]
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
155 }
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
156
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
157
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
158
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
159 #elif str($pixels_cond.pixel_filtering) == "none":
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
160 print("no pixel filtering")
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
161 numberpixels = 0
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
162 validpixels = 0
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
163
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
164 #end if
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
165
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
166
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
167
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
168 ###################################### filtering of features ######################
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
169
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
170 #if str($features_cond.features_filtering) == "features_list":
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
171
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
172 print("feature list")
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
173
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
174 input_features = read.delim("$inputfeatures", header = FALSE, stringsAsFactors = FALSE)
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
175
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
176 startingrow = $features_cond.feature_header+1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
177 extracted_features = input_features[startingrow:nrow(input_features),$features_cond.feature_column]
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
178 numberfeatures = length(extracted_features)
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
179
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
180
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
181 if (grepl("m/z = ", input_features[startingrow,$features_cond.feature_column])==FALSE)
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
182
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
183 { print("no m/z = in data")
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
184
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
185 if (class(extracted_features) == "numeric")
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
186 {
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
187 charactervector = rep("m/z = ", numberfeatures)
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
188 mz_added = paste0(charactervector, round(extracted_features,digits=2))
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
189 validfeatures = mz_added %in% names(features(msidata))
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
190 featuresofinterest = features(msidata)[names(features(msidata)) %in% mz_added[validfeatures]]
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
191 }else{
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
192 validfeatures = 0
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
193 featuresofinterest = features(msidata)
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
194 }
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
195 }else{
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
196 validfeatures = extracted_features %in% names(features(msidata))
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
197 featuresofinterest = features(msidata)[names(features(msidata)) %in% extracted_features[validfeatures]]
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
198 }
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
199
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
200 msidata = msidata[featuresofinterest,]
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
201
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
202
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
203
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
204 #elif str($features_cond.features_filtering) == "features_range":
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
205
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
206 print("feature range")
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
207
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
208 numberfeatures = "range"
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
209 validfeatures = NA
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
210
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
211 if (sum(mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz)> 0)
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
212 {
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
213 msidata = msidata[mz(msidata) >= $features_cond.min_mz & mz(msidata) <= $features_cond.max_mz,]
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
214 }
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
215
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
216
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
217 #elif str($features_cond.features_filtering) == "none":
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
218
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
219 print("no feature filtering")
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
220 validfeatures = 0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
221 numberfeatures = 0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
222 #end if
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
223
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
224
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
225
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
226 # save msidata as Rfile
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
227 save(msidata, file="$msidata_filtered")
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
228
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
229 ###################################### outputfile properties in numbers ######################
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
230
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
231 #if $outputs.outputs_select == "quality_control":
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
232
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
233 ## Number of features (mz)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
234 maxfeatures2 = length(features(msidata))
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
235 ## Range mz
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
236 minmz2 = round(min(mz(msidata)), digits=2)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
237 maxmz2 = round(max(mz(msidata)), digits=2)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
238 ## Number of spectra (pixels)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
239 pixelcount2 = length(pixels(msidata))
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
240 ## Range x coordinates
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
241 minimumx2 = min(coord(msidata)[,1])
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
242 maximumx2 = max(coord(msidata)[,1])
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
243 ## Range y coordinates
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
244 minimumy2 = min(coord(msidata)[,2])
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
245 maximumy2 = max(coord(msidata)[,2])
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
246 ## Number of intensities > 0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
247 npeaks2= sum(spectra(msidata)[]>0)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
248 ## Spectra multiplied with mz (potential number of peaks)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
249 numpeaks2 = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
250 ## Percentage of intensities > 0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
251 percpeaks2 = round(npeaks2/numpeaks2*100, digits=2)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
252 ## Number of empty TICs
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
253 TICs2 = colSums(spectra(msidata)[])
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
254 NumemptyTIC2 = sum(TICs2 == 0)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
255 ## median TIC
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
256 medint2 = round(median(TICs2), digits=2)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
257
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
258
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
259 properties = c("Number of mz features",
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
260 "Range of mz values [Da]",
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
261 "Number of pixels",
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
262 "Range of x coordinates",
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
263 "Range of y coordinates",
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
264 "Intensities > 0",
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
265 "Median TIC per pixel",
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
266 "Number of zero TICs",
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
267 "pixel overview",
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
268 "feature overview")
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
269
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
270 before = c(paste0(maxfeatures),
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
271 paste0(minmz, " - ", maxmz),
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
272 paste0(pixelcount),
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
273 paste0(minimumx, " - ", maximumx),
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
274 paste0(minimumy, " - ", maximumy),
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
275 paste0(percpeaks, " %"),
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
276 paste0(medint),
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
277 paste0(NumemptyTIC),
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
278 paste0("input pixels: ", numberpixels),
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
279 paste0("input mz: ", numberfeatures))
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
280
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
281 filtered = c(paste0(maxfeatures2),
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
282 paste0(minmz2, " - ", maxmz2),
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
283 paste0(pixelcount2),
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
284 paste0(minimumx2, " - ", maximumx2),
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
285 paste0(minimumy2, " - ", maximumy2),
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
286 paste0(percpeaks2, " %"),
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
287 paste0(medint2),
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
288 paste0(NumemptyTIC2),
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
289 paste0("valid pixels: ", validpixels),
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
290 paste0("valid mz: ", sum(validfeatures)))
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
291
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
292
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
293 property_df = data.frame(properties, before, filtered)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
294
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
295
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
296
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
297 ######################################## PDF QC #############################################
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
298
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
299 pdf("filtertool_QC.pdf", fonts = "Times", pointsize = 12)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
300 plot(0,type='n',axes=FALSE,ann=FALSE)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
301
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
302 title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.display_name"))
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
303
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
304
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
305
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
306 grid.table(property_df, rows= NULL)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
307
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
308 ### heatmap image as visual pixel control
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
309
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
310 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0)
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
311 {
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
312
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
313
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
314 image(msidata, mz=$outputs.inputmz, plusminus = $outputs.plusminus_dalton, contrast.enhance = "none",
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
315 main= paste0($outputs.inputmz," ± ", $outputs.plusminus_dalton, " Da"), ylim = c(maximumy2+0.2*maximumy2,minimumy2-0.2*minimumy2))
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
316
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
317 ### control features which are left
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
318
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
319 plot(featuresinfile, rep(1,length(featuresinfile)), yaxt="n", ylab=NA, xlab="m/z values", col="red", ylim=c(0.8, 1.1), main="Distribution of m/z values")
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
320 lines(mz(msidata),rep(0.9, length(mz(msidata))), col="green", type="p")
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
321 legend("top", horiz=TRUE,
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
322 legend = c("before", "filtered"),
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
323 fill = c("red", "green"))
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
324
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
325
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
326
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
327
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
328 }else{
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
329 print("file has no features or pixels left")
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
330 }
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
331
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
332 dev.off()
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
333
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
334 #end if
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
335
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
336 ######################################## intensity matrix ##################################
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
337
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
338 #if $output_matrix:
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
339
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
340 if (length(features(msidata))> 0 & length(pixels(msidata)) > 0)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
341 {
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
342
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
343 spectramatrix = spectra(msidata)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
344 rownames(spectramatrix) = mz(msidata)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
345 newmatrix = rbind(pixels(msidata), spectramatrix)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
346 write.table(newmatrix[2:nrow(newmatrix),], file="$matrixasoutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t")
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
347
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
348 }else{
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
349 print("file has no features or pixels left")
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
350 }
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
351
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
352 #end if
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
353
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
354
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
355 ]]></configfile>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
356 </configfiles>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
357 <inputs>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
358 <param name="infile" type="data" format="imzml, rdata, analyze75"
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
359 label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
360 help="Upload composite datatype imzML (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
361
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
362 <conditional name="pixels_cond">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
363 <param name="pixel_filtering" type="select" label="Select pixel filtering option">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
364 <option value="none" selected="True">none</option>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
365 <option value="single_column">tabular file with single column (x = 1, y = 1)</option>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
366 <option value="two_columns">tabular file with separate columns for x and y values</option>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
367 <option value="pixel_range">ranges for x and y</option>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
368 </param>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
369 <when value="none"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
370 <when value="single_column">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
371 <param name="single_pixels" type="data" format="tabular" label="Pixels in single column for filtering of MSI data"
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
372 help="tabular file with pixels of interest in the form x = 1, y = 1"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
373 <param name="pixel_column" data_ref="single_pixels" label="Column with pixels" type="data_column"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
374 </when>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
375 <when value="two_columns">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
376 <param name="two_columns_pixel" type="data" format="tabular" label="Pixels in two columns for filtering of MSI data"
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
377 help="tabular file with pixels of interest in two separate columns"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
378 <param name="pixel_column_x" data_ref="two_columns_pixel" label="Column with x values" type="data_column"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
379 <param name="pixel_column_y" data_ref="two_columns_pixel" label="Column with y values" type="data_column"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
380 </when>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
381 <when value="pixel_range">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
382 <param name="min_x_range" type="integer" value="0" label="Minimum value for x"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
383 <param name="max_x_range" type="integer" value="100" label="Maximum value for x"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
384 <param name="min_y_range" type="integer" value="0" label="Minimum value for y"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
385 <param name="max_y_range" type="integer" value="100" label="Maximum value for y"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
386 </when>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
387 </conditional>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
388
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
389 <conditional name="features_cond">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
390 <param name="features_filtering" type="select" label="Select feature filtering option">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
391 <option value="none" selected="True">none</option>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
392 <option value="features_list">tabular file with features (data type: 800.12 or m/z = 800.12)</option>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
393 <option value="features_range">range of features</option>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
394 </param>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
395
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
396 <when value="none"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
397 <when value="features_list">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
398 <param name="inputfeatures" type="data" format="tabular" label="Features for filtering of MSI data" help="tabular file with masses of interest either as numbers (800.05) or in the form m/z = 800.05"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
399 <param name="feature_column" data_ref="inputfeatures" label="Column with features" type="data_column"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
400 <param name="feature_header" label="Number of header lines to skip" value="0" type="integer"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
401 </when>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
402 <when value="features_range">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
403 <param name="min_mz" type="integer" value="1" label="Minimum value for mz (in Dalton)"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
404 <param name="max_mz" type="integer" value="100" label="Maximum value for mz (in Dalton)"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
405 </when>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
406 </conditional>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
407
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
408 <conditional name="outputs">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
409 <param name="outputs_select" type="select" label="Quality control output">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
410 <option value="quality_control" selected="True">yes</option>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
411 <option value="no_quality_control">no</option>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
412 </param>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
413 <when value="quality_control">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
414 <param name="inputmz" type="float" value="1296.7" label="Mass for which a heatmap image will be drawn" help="Use a mass which is still present in all pixels to control if the pixel filtering went well"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
415 <param name="plusminus_dalton" value="0.25" type="float" label="mass range for mz value" help="plusminus mass window in Dalton"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
416 </when>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
417 <when value="no_quality_control"/>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
418 </conditional>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
419 <param name="output_matrix" type="boolean" display="radio" label="Intensity matrix output"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
420 </inputs>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
421 <outputs>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
422 <data format="rdata" name="msidata_filtered" label="${tool.name} ${on_string}"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
423 <data format="pdf" name="filtering_qc" from_work_dir="filtertool_QC.pdf" label = "QC ${tool.name} ${on_string}">
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
424 <filter>outputs["outputs_select"] == "quality_control"</filter>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
425 </data>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
426 <data format="tabular" name="matrixasoutput" label="Matrix ${tool.name} on ${on_string}">
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
427 <filter>output_matrix</filter>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
428 </data>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
429 </outputs>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
430
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
431 <tests>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
432 <test expect_num_outputs="2">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
433 <param name="infile" value="" ftype="imzml">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
434 <composite_data value="Example_Continuous.imzML"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
435 <composite_data value="Example_Continuous.ibd"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
436 </param>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
437 <param name="pixel_filtering" value="single_column"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
438 <param name="single_pixels" ftype="tabular" value = "inputpixels.tabular"/>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
439 <param name="pixel_column" value="1"/>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
440 <param name="features_filtering" value="features_list"/>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
441 <param name="inputfeatures" ftype="tabular" value = "inputfeatures.tabular"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
442 <param name="feature_column" value="2"/>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
443 <param name="feature_header" value="1"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
444 <param name="outputs_select" value="quality_control"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
445 <param name="inputmz" value="328.9"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
446 <param name="plusminus_dalton" value="0.25"/>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
447 <output name="filtering_qc" file="imzml_filtered.pdf" compare="sim_size" delta="20000"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
448 <output name="msidata_filtered" file="imzml_filtered.RData" compare="sim_size" />
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
449 </test>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
450 <test expect_num_outputs="2">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
451 <param name="infile" value="" ftype="imzml">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
452 <composite_data value="Example_Continuous.imzML"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
453 <composite_data value="Example_Continuous.ibd"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
454 </param>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
455 <param name="pixel_filtering" value="pixel_range"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
456 <param name="min_x_range" value="0"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
457 <param name="max_x_range" value="10"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
458 <param name="min_y_range" value="2"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
459 <param name="max_y_range" value="2"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
460 <param name="outputs_select" value="quality_control"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
461 <param name="inputmz" value="328.9"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
462 <param name="plusminus_dalton" value="0.25"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
463 <output name="filtering_qc" file="imzml_filtered2.pdf" compare="sim_size" delta="20000"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
464 <output name="msidata_filtered" file="imzml_filtered2.RData" compare="sim_size" />
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
465 </test>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
466 <test expect_num_outputs="3">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
467 <param name="infile" value="" ftype="imzml">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
468 <composite_data value="Example_Continuous.imzML"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
469 <composite_data value="Example_Continuous.ibd"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
470 </param>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
471 <param name="pixel_filtering" value="pixel_range"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
472 <param name="min_x_range" value="0"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
473 <param name="max_x_range" value="10"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
474 <param name="min_y_range" value="2"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
475 <param name="max_y_range" value="2"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
476 <param name="features_filtering" value="features_range"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
477 <param name="min_mz" value="200" />
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
478 <param name="max_mz" value="500"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
479 <param name="outputs_select" value="quality_control"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
480 <param name="inputmz" value="328.9"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
481 <param name="plusminus_dalton" value="0.25"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
482 <param name="output_matrix" value="True"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
483 <output name="filtering_qc" file="imzml_filtered3.pdf" compare="sim_size" delta="20000"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
484 <output name="msidata_filtered" file="imzml_filtered3.RData" compare="sim_size" />
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
485 <output name="matrixasoutput" file="imzml_matrix3.tabular"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
486 </test>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
487 <test expect_num_outputs="2">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
488 <param name="infile" value="" ftype="imzml">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
489 <composite_data value="Example_Continuous.imzML"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
490 <composite_data value="Example_Continuous.ibd"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
491 </param>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
492 <param name="pixel_filtering" value="two_columns"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
493 <param name="two_columns_pixel" ftype="tabular" value = "inputpixels_2column.tabular"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
494 <param name="pixel_column_x" value="1"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
495 <param name="pixel_column_y" value="3"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
496 <param name="features_filtering" value="features_list"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
497 <param name="inputfeatures" ftype="tabular" value = "inputcalibrantfile2.txt"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
498 <param name="feature_column" value="1"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
499 <param name="feature_header" value="0"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
500 <param name="outputs_select" value="quality_control"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
501 <param name="inputmz" value="328.9"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
502 <param name="plusminus_dalton" value="0.25"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
503 <output name="filtering_qc" file="imzml_filtered4.pdf" compare="sim_size" delta="20000"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
504 <output name="msidata_filtered" file="imzml_filtered4.RData" compare="sim_size" />
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
505 </test>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
506 <test expect_num_outputs="2">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
507 <param name="infile" value="" ftype="imzml">
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
508 <composite_data value="Example_Continuous.imzML"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
509 <composite_data value="Example_Continuous.ibd"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
510 </param>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
511 <param name="pixel_filtering" value="pixel_range"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
512 <param name="min_x_range" value="0"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
513 <param name="max_x_range" value="10"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
514 <param name="min_y_range" value="2"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
515 <param name="max_y_range" value="20"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
516 <param name="features_filtering" value="features_range"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
517 <param name="min_mz" value="1" />
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
518 <param name="max_mz" value="150"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
519 <param name="outputs_select" value="quality_control"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
520 <param name="inputmz" value="328.9"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
521 <param name="plusminus_dalton" value="0.25"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
522 <output name="filtering_qc" file="imzml_filtered5.pdf" compare="sim_size" delta="20000"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
523 <output name="msidata_filtered" file="imzml_filtered5.RData" compare="sim_size" />
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
524 </test>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
525 <test expect_num_outputs="3">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
526 <param name="infile" value="" ftype="analyze75">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
527 <composite_data value="Analyze75.hdr"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
528 <composite_data value="Analyze75.img"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
529 <composite_data value="Analyze75.t2m"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
530 </param>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
531 <param name="pixel_filtering" value="single_column"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
532 <param name="single_pixels" ftype="tabular" value = "inputpixels2.tabular"/>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
533 <param name="pixel_column" value="1"/>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
534 <param name="features_filtering" value="features_list"/>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
535 <param name="inputfeatures" ftype="tabular" value = "featuresofinterest2.tabular"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
536 <param name="feature_column" value="1"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
537 <conditional name="outputs">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
538 <param name="outputs_select" value="quality_control"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
539 <param name="inputmz" value="702"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
540 <param name="plusminus_dalton" value="0.25"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
541 </conditional>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
542 <param name="output_matrix" value="True"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
543 <output name="filtering_qc" file="analyze_filtered.pdf" compare="sim_size" delta="20000"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
544 <output name="msidata_filtered" file="analyze_filtered.RData" compare="sim_size" />
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
545 <output name="matrixasoutput" file="analyze_matrix.tabular"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
546 </test>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
547 <test expect_num_outputs="2">
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
548 <param name="infile" value="" ftype="analyze75">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
549 <composite_data value="Analyze75.hdr"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
550 <composite_data value="Analyze75.img"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
551 <composite_data value="Analyze75.t2m"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
552 </param>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
553 <conditional name="outputs">
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
554 <param name="outputs_select" value="quality_control"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
555 <param name="inputmz" value="702"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
556 <param name="plusminus_dalton" value="0.25"/>
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
557 </conditional>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
558 <output name="filtering_qc" file="analyze75_filtered2.pdf" compare="sim_size" delta="20000"/>
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
559 <output name="msidata_filtered" file="analyze_originaloutput2.RData" compare="sim_size" />
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
560 </test>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
561 <test expect_num_outputs="2">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
562 <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
563 <conditional name="outputs">
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
564 <param name="outputs_select" value="no_quality_control"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
565 </conditional>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
566 <param name="output_matrix" value="True"/>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
567 <output name="matrixasoutput" file="rdata_matrix.tabular"/>
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
568 <output name="msidata_filtered" file="rdata_notfiltered.RData" compare="sim_size" />
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
569 </test>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
570 </tests>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
571 <help>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
572 <![CDATA[
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
573
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
574 This tool can filter three types of mass-spectrometry imaging files (see below) for pixels and features of interest. This can be used to keep only pixels in a regions of interest.
1
98c101b19f3c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 0
diff changeset
575 For filtering at least one valid pixel/feature is needed otherwise no filtering will be performed. It is recommended to use the filtering tool only for feature masses which have been extracted from the same dataset. If you have feature masses from dataset A and you want to use them to filter dataset B, first find the corresponding (closest) features in dataset B by using the tool "Join two files on column allowing a small difference". Afterwards use the corresponding feature masses from dataset B to filter dataset B.
0
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
576
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
577 Input data: 3 types of input data can be used:
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
578
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
579 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <http://ms-imaging.org/wp/introduction/>`_
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
580 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
581 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
582
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
583 The output of this tool is a subsetted Cardinal "MSImageSet" with the variable name "msidata" saved as .RData.
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
584 ]]>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
585 </help>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
586 <citations>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
587 <citation type="doi">10.1093/bioinformatics/btv146</citation>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
588 </citations>
f17d3f1a065f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_filtering commit 3363c40790b0d64a085f980980f4289165eed27f
galaxyp
parents:
diff changeset
589 </tool>