Mercurial > repos > galaxyp > cardinal_mz_images

annotate macros.xml @ 15:5629069fca8f draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
author galaxyp
date Sun, 29 Aug 2021 07:35:34 +0000
parents 7828af552085
children c4df3005e04d
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rev   line source
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25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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1 <macros>
15
5629069fca8f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit c8d3adac445b4e08e2724e22d7201bfc38bbf40f"
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2 <token name="@VERSION@">2.10.0</token>
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25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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4 <xml name="requirements">
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5 <requirements>
25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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6 <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement>
9
08ebd8da780c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
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7 <!--requirement type="package" version="3.6.1">r-base</requirement-->
6
25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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8 <yield/>
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9 </requirements>
25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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10 </xml>
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25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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12 <xml name="print_version">
25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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13 <version_command><![CDATA[
25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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14 echo $(R --version | grep version | grep -v GNU)", Cardinal version" $(R --vanilla --slave -e "library(Cardinal); cat(sessionInfo()\$otherPkgs\$Cardinal\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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15 ]]></version_command>
25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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16 </xml>
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25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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18 <token name="@INPUT_LINKING@"><![CDATA[
25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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19 #if $infile.ext == 'imzml'
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20 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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21 ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
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22 #elif $infile.ext == 'analyze75'
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23 ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
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24 ln -s '${infile.extra_files_path}/img' infile.img &&
25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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25 ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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26 #else
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27 ln -s $infile infile.RData &&
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28 #end if
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29 ]]></token>
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25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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32 <token name="@READING_MSIDATA@"><![CDATA[
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33 ## importing MSI data files
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34
8
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35 ## read RData files (MSI and other data) independent of filename
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36 loadRData <- function(fileName){
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37 load(fileName)
a69865da6f80 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
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38 get(ls()[ls() != "fileName"])
a69865da6f80 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
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39 }
a69865da6f80 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
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40
6
25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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41 #if $infile.ext == 'imzml'
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42 #if str($processed_cond.processed_file) == "processed":
7
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43 msidata <- readImzML('infile', resolution=$processed_cond.accuracy, attach.only=TRUE, units = "$processed_cond.units")
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44 msidata = collect(msidata, as.matrix=TRUE) ##coercion to continuous
6
25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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45 centroided(msidata) = $centroids
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46 #else
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47 msidata <- readImzML('infile', attach.only=TRUE)
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48 centroided(msidata) = $centroids
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49 #end if
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50 #elif $infile.ext == 'analyze75'
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51 msidata = readAnalyze('infile', attach.only=TRUE)
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52 centroided(msidata) = $centroids
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53 #else
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54 msidata = loadRData('infile.RData')
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55 #end if
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56
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57 ]]></token>
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58
25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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59 <token name="@DATA_PROPERTIES@"><![CDATA[
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60 ## Number of features (mz)
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61 maxfeatures = length(features(msidata))
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62 ## Range mz
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63 minmz = round(min(mz(msidata)), digits=2)
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64 maxmz = round(max(mz(msidata)), digits=2)
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65 ## Number of spectra (pixels)
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66 pixelcount = length(pixels(msidata))
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67 ## Range x coordinates
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68 minimumx = min(coord(msidata)[,1])
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69 maximumx = max(coord(msidata)[,1])
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70 ## Range y coordinates
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71 minimumy = min(coord(msidata)[,2])
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72 maximumy = max(coord(msidata)[,2])
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73
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74
25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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75 properties = c("Number of m/z features",
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76 "Range of m/z values",
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77 "Number of pixels",
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78 "Range of x coordinates",
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79 "Range of y coordinates")
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80
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81 values = c(paste0(maxfeatures),
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82 paste0(minmz, " - ", maxmz),
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83 paste0(pixelcount),
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84 paste0(minimumx, " - ", maximumx),
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85 paste0(minimumy, " - ", maximumy))
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86
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87 property_df = data.frame(properties, values)
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88 ]]></token>
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89
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90 <token name="@READING_MSIDATA_FULLY_COMPATIBLE@"><![CDATA[
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91 ## importing MSI data files
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92
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93 #if $infile.ext == 'imzml'
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94 #if str($processed_cond.processed_file) == "processed":
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95 msidata <- readImzML('infile', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE)
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96 centroided(msidata) = $centroids
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97 #else
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98 msidata <- readImzML('infile', attach.only=TRUE)
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99 centroided(msidata) = $centroids
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100 #end if
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101 #elif $infile.ext == 'analyze75'
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102 msidata = readAnalyze('infile', attach.only=TRUE)
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103 centroided(msidata) = $centroids
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104 #else
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105 ## function to read RData files independent of filename
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106 loadRData <- function(fileName){
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107 load(fileName)
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108 get(ls()[ls() != "fileName"])
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109 }
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110 msidata = loadRData('infile.RData')
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111 msidata = as(msidata, "MSImagingExperiment")
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112 run(msidata) = "infile"
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113 #end if
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114
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115 ]]></token>
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116
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117 <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[
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118 ########################### QC numbers ########################
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119 ## including intensity calculations which need data in RAM
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120
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121 int_matrix = as.matrix(spectra(msidata)) ## only load once into RAM, then re-use
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122 ## Number of NA in spectra matrix
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123 NAcount = sum(is.na(int_matrix))
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124 ## replace NA with zero to calculate data properties based on intensity matrix, no change in msidata
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125 int_matrix[is.na(int_matrix)] <- 0
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126
6
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127 ## Number of features (mz)
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128 maxfeatures = length(features(msidata))
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129 ## Range mz
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130 minmz = round(min(mz(msidata)), digits=2)
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131 maxmz = round(max(mz(msidata)), digits=2)
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132 ## Number of spectra (pixels)
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133 pixelcount = length(pixels(msidata))
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134 ## Range x coordinates
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135 minimumx = min(coord(msidata)[,1])
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136 maximumx = max(coord(msidata)[,1])
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137 ## Range y coordinates
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138 minimumy = min(coord(msidata)[,2])
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139 maximumy = max(coord(msidata)[,2])
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140 ## Range of intensities
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141 minint = round(min(int_matrix), digits=2)
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142 maxint = round(max(int_matrix), digits=2)
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143 ## Number of intensities > 0, for if conditions
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144 npeaks= sum(int_matrix>0)
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145 ## Number of NA in spectra matrix
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146 infcount = sum(is.infinite(int_matrix))
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147 ## Number of duplicated coordinates
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148 dupl_coord = sum(duplicated(coord(msidata)))
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149 properties = c("Number of m/z features",
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150 "Range of m/z values",
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151 "Number of pixels",
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152 "Range of x coordinates",
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153 "Range of y coordinates",
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154 "Range of intensities",
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155 "Number of NA intensities",
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156 "Number of Inf intensities",
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157 "Number of duplicated coordinates")
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158
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159 values = c(paste0(maxfeatures),
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160 paste0(minmz, " - ", maxmz),
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161 paste0(pixelcount),
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162 paste0(minimumx, " - ", maximumx),
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163 paste0(minimumy, " - ", maximumy),
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164 paste0(minint, " - ", maxint),
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165 paste0(NAcount),
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166 paste0(infcount),
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167 paste0(dupl_coord))
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168
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169 property_df = data.frame(properties, values)
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170 ]]></token>
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171
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172 <token name="@CARDINAL_DESCRIPTION@"><![CDATA[
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173 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets.
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174 `More information on Cardinal <http://cardinalmsi.org/>`_
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175 ]]></token>
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176 <token name="@MSIDATA_INPUT_DESCRIPTION@"><![CDATA[
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177 **Input data**
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178
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179 - MSI data: 3 types of input data can be used:
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180
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181 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
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182 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
9
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183 - Cardinal "MSImageSet" or "MSImagingExperiment" saved as .RData
6
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184 ]]></token>
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185 <token name="@MZ_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
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186 - Optional tabular file with m/z values:
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187
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188 - One column with numeric m/z values (without empty fields or letters)
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189 - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
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190 - m/z features outside the m/z range of the input file are ignored
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191
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192
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193 ::
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194
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195 m/z
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196 100.0
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197 100.01
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198 100.02
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199 ...
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200 ...
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201
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202 ]]></token>
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203 <token name="@MZ_2COLS_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
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204 - Tabular file with m/z values:
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205
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206 - One column with numeric m/z values (without empty fields or letters), another column with names for the m/z (m/z column can also be used as name)
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207 - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
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208 - m/z features outside the m/z range of the input file are ignored
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209
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210
25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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211 ::
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212
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213 m/z name
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214 100.0 analyte1
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215 100.01 analyte2
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216 100.02 analyte3
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217 ...
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218 ...
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219
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220 ]]></token>
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221 <token name="@SPECTRA_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
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222 - Optional file with pixel coordinates and annotation:
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223
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224 - Tabular file: One column with x values, one column with y values and one column with annotations
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225 - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
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226 - Pixel with coordinates outside the coordinates of the input file are ignored
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227
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228 ::
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229
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230 x_coord y_coord annotation
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231 1 1 healthy
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232 2 1 healthy
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233 3 1 disease
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234 ...
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235 ...
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236
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237 ]]></token>
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238
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239 <xml name="reading_msidata">
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240 <param name="infile" type="data" format="imzml,rdata,analyze75"
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241 label="MSI data"
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242 help="Input file as imzML (composite upload), Analyze7.5 (composite upload) or Cardinal MSImageSet saved as RData (regular upload)"/>
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243 <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/>
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244 <conditional name="processed_cond">
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245 <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file">
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246 <option value="no_processed" selected="True">no</option>
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247 <option value="processed">yes</option>
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248 </param>
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249 <when value="no_processed"/>
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250 <when value="processed">
9
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251 <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned"/>
6
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252 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
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253 <option value="mz" >mz</option>
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254 <option value="ppm" selected="True" >ppm</option>
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255 </param>
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256 </when>
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257 </conditional>
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258 </xml>
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259
25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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260 <xml name="pdf_filename">
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261 <param name="filename" type="text" value="" label="Title" help="Will appear in the pdf output, if nothing given it will take the dataset name">
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262 <sanitizer invalid_char="">
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263 <valid initial="string.ascii_letters,string.digits">
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264 <add value="_"/>
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265 <add value=" "/>
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266 </valid>
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267 </sanitizer>
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268 </param>
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269 </xml>
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270
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271 <xml name="sanitizer_multiple_digits">
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272 <sanitizer invalid_char="">
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273 <valid initial="string.digits">
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274 <add value=":" />
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275 <add value="," />
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276 </valid>
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277 </sanitizer>
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278 </xml>
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279
25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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280 <xml name="reading_1_column_mz_tabular" token_label="Tabular file with m/z features">
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281 <param name="mz_tabular" type="data" format="tabular" label="@LABEL@" help="Only numeric m/z values are allowed"/>
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282 <param name="feature_column" data_ref="mz_tabular" label="Column with features" type="data_column"/>
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283 <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
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284 </xml>
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285
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286 <xml name="reading_2_column_mz_tabular" token_optional="false">
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287 <param name="calibrant_file" type="data" optional="@OPTIONAL@" format="tabular"
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288 label="m/z of interest (e.g. internal Calibrants)" help="one column with m/z values, optional second column with names (m/z values can also be selected as name)"/>
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289 <param name="mz_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with m/z values" type="data_column"/>
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290 <param name="name_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with name of m/z values" type="data_column"/>
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291 <param name="calibrant_header" type="boolean" optional="@OPTIONAL@" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
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292 </xml>
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293
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294 <xml name="reading_pixel_annotations">
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295 <param name="annotation_file" type="data" format="tabular" label="Tabular file with pixel coordinates and annotation"
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296 help="Tabular file with three columns: x values, y values and pixel annotations"/>
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297 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
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298 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
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299 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>
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300 <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
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301 </xml>
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302
25b83cbd596a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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303 <xml name="citations">
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304 <citations>
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305 <citation type="doi">10.1093/bioinformatics/btv146</citation>
7
5e6f8fb2df07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
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306 <citation type="doi">10.1093/gigascience/giz143</citation>
6
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307 </citations>
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308 </xml>
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309 <xml name="infile_analyze75">
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310 <param name="infile" value="" ftype="analyze75">
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311 <composite_data value="Analyze75.hdr"/>
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312 <composite_data value="Analyze75.img"/>
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313 <composite_data value="Analyze75.t2m"/>
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314 </param>
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315 </xml>
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316 <xml name="infile_imzml">
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317 <param name="infile" value="" ftype="imzml">
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318 <composite_data value="Example_Continuous.imzML"/>
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319 <composite_data value="Example_Continuous.ibd"/>
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320 </param>
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321 </xml>
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322 <xml name="processed_infile_imzml">
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323 <param name="infile" value="" ftype="imzml">
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324 <composite_data value="Example_Processed.imzML"/>
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325 <composite_data value="Example_Processed.ibd"/>
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326 </param>
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327 </xml>
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328 </macros>