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comparison filtering.xml @ 7:1d4a6fe69a40 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
author galaxyp
date Thu, 23 Apr 2020 08:10:44 -0400
parents d2ccd8348018
children e92efed83208
comparison
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6:d2ccd8348018 7:1d4a6fe69a40
1 <tool id="cardinal_filtering" name="MSI filtering" version="2.4.0.0"> 1 <tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.0">
2 <description>tool for filtering mass spectrometry imaging data</description> 2 <description>tool for filtering mass spectrometry imaging data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <expand macro="requirements">
7 <requirement type="package" version="2.4.0">bioconductor-cardinal</requirement>
8 <requirement type="package" version="3.6.1">r-base</requirement>
9 <requirement type="package" version="2.3">r-gridextra</requirement> 7 <requirement type="package" version="2.3">r-gridextra</requirement>
10 <requirement type="package" version="3.2.1">r-ggplot2</requirement> 8 <requirement type="package" version="3.2.1">r-ggplot2</requirement>
11 </requirements> 9 </expand>
12 <expand macro="print_version"/> 10 <expand macro="print_version"/>
13 <command detect_errors="exit_code"> 11 <command detect_errors="exit_code">
14 <![CDATA[ 12 <![CDATA[
15 13
16 @INPUT_LINKING@ 14 @INPUT_LINKING@
36 library(ggplot2) 34 library(ggplot2)
37 library(gridExtra) 35 library(gridExtra)
38 36
39 37
40 38
41 ## function to read RData files independent of filename 39 @READING_MSIDATA_FULLY_COMPATIBLE@
42 loadRData <- function(fileName){
43 load(fileName)
44 get(ls()[ls() != "fileName"])
45 }
46
47 #if $infile.ext == 'imzml'
48 #if str($processed_cond.processed_file) == "processed":
49 msidata <- readImzML('infile', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE)
50 centroided(msidata) = $centroids
51 #else
52 msidata <- readImzML('infile', attach.only=TRUE)
53 centroided(msidata) = $centroids
54 #end if
55 #elif $infile.ext == 'analyze75'
56 msidata = readAnalyze('infile', attach.only=TRUE)
57 centroided(msidata) = $centroids
58 #else
59 msidata = loadRData('infile.RData')
60 msidata = as(msidata, "MSImagingExperiment")
61 #end if
62 40
63 41
64 ########################### QC numbers ######################## 42 ########################### QC numbers ########################
65 43
66 ## Number of features (m/z) 44 ## Number of features (m/z)