Mercurial > repos > galaxyp > cardinal_combine
comparison combine.xml @ 20:a9a28e46d54a draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
| author | galaxyp |
|---|---|
| date | Thu, 04 Jul 2024 13:47:49 +0000 |
| parents | aad328eb6c0f |
| children |
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| 19:bf06d196e23d | 20:a9a28e46d54a |
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| 1 <tool id="cardinal_combine" name="MSI combine" version="@VERSION@.0"> | 1 <tool id="cardinal_combine" name="MSI combine" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> |
| 2 <description> | 2 <description> |
| 3 combine several mass spectrometry imaging datasets into one | 3 combine several mass spectrometry imaging datasets into one |
| 4 </description> | 4 </description> |
| 5 <macros> | 5 <macros> |
| 6 <import>macros.xml</import> | 6 <import>macros.xml</import> |
| 7 </macros> | 7 </macros> |
| 8 <expand macro="requirements"> | 8 <expand macro="requirements"/> |
| 9 <requirement type="package" version="3.3.5">r-ggplot2</requirement> | |
| 10 <requirement type="package" version="0.12">r-maldiquantforeign</requirement> | |
| 11 <requirement type="package" version="1.20">r-maldiquant</requirement> | |
| 12 </expand> | |
| 13 <command detect_errors="exit_code"> | 9 <command detect_errors="exit_code"> |
| 14 <![CDATA[ | 10 <![CDATA[ |
| 15 #for $i, $infile in enumerate($infiles): | 11 #for $i, $infile in enumerate($infiles): |
| 16 #if $infile.ext == 'imzml' | 12 #if $infile.ext == 'imzml' |
| 17 ln -s '${infile.extra_files_path}/imzml' infile_${i}.imzML && | 13 cp '${infile.extra_files_path}/imzml' infile_${i}.imzML && |
| 18 ln -s '${infile.extra_files_path}/ibd' infile_${i}.ibd && | 14 cp '${infile.extra_files_path}/ibd' infile_${i}.ibd && |
| 19 #elif $infile.ext == 'analyze75' | 15 #elif $infile.ext == 'analyze75' |
| 20 ln -s '${infile.extra_files_path}/hdr' infile_${i}.hdr && | 16 cp '${infile.extra_files_path}/hdr' infile_${i}.hdr && |
| 21 ln -s '${infile.extra_files_path}/img' infile_${i}.img && | 17 cp '${infile.extra_files_path}/img' infile_${i}.img && |
| 22 ln -s '${infile.extra_files_path}/t2m' infile_${i}.t2m && | 18 cp '${infile.extra_files_path}/t2m' infile_${i}.t2m && |
| 23 #else | 19 #else |
| 24 ln -s '$infile' infile_${i}.RData && | 20 ln -s '$infile' infile_${i}.RData && |
| 25 #end if | 21 #end if |
| 26 #end for | 22 #end for |
| 27 #if $annotation_cond.annotation_tabular == 'annotation' | 23 #if $annotation_cond.annotation_tabular == 'annotation' |
| 101 loadRData <- function(fileName){ | 97 loadRData <- function(fileName){ |
| 102 load(fileName) | 98 load(fileName) |
| 103 get(ls()[ls() != "fileName"]) | 99 get(ls()[ls() != "fileName"]) |
| 104 } | 100 } |
| 105 msidata_$i = loadRData('infile_${i}.RData') | 101 msidata_$i = loadRData('infile_${i}.RData') |
| 106 ## keep compatibility with old .RData files: | |
| 107 msidata_$i\$column1 = NULL | |
| 108 msidata_$i\$column2 = NULL | |
| 109 msidata_$i\$column3 = NULL | |
| 110 msidata_$i\$column4 = NULL | |
| 111 msidata_$i\$column5 = NULL | |
| 112 msidata_$i\$combined_sample = NULL | |
| 113 msidata_$i <- as(msidata_$i, "MSImagingExperiment") | 102 msidata_$i <- as(msidata_$i, "MSImagingExperiment") |
| 103 | |
| 114 #end if | 104 #end if |
| 115 | 105 |
| 116 ## remove duplicated coordinates, otherwise combine will fail | 106 ## remove duplicated coordinates, otherwise combine will fail |
| 117 print(paste0(sum(duplicated(coord(msidata_$i))), " duplicated coordinates were removed from input file")) | 107 print(paste0(sum(duplicated(coord(msidata_$i))), " duplicated coordinates were removed from input file")) |
| 118 msidata_${i} <- msidata_${i}[,!duplicated(coord(msidata_${i}))] | 108 msidata_${i} <- msidata_${i}[,!duplicated(coord(msidata_${i}))] |
| 126 pData(msidata_${i})\$'3DPositionY' <- NULL | 116 pData(msidata_${i})\$'3DPositionY' <- NULL |
| 127 | 117 |
| 128 ############ 3) Read and process annotation tabular files ###################### | 118 ############ 3) Read and process annotation tabular files ###################### |
| 129 | 119 |
| 130 #if str($annotation_cond.annotation_tabular) == 'annotation' | 120 #if str($annotation_cond.annotation_tabular) == 'annotation' |
| 131 print("annotations") | |
| 132 | 121 |
| 133 ## read annotation tabular, set first two columns as x and y, merge with coordinates dataframe and order according to pixelorder in msidata | 122 ## read annotation tabular, set first two columns as x and y, merge with coordinates dataframe and order according to pixelorder in msidata |
| 134 input_annotation = read.delim("annotation_file_${i}.tabular", header = $annotation_cond.tabular_header, stringsAsFactors = FALSE) | 123 input_annotation = read.delim("annotation_file_${i}.tabular", header = $annotation_cond.tabular_header, stringsAsFactors = FALSE) |
| 135 colnames(input_annotation)[1:2] = c("x", "y") | 124 colnames(input_annotation)[1:2] = c("x", "y") |
| 136 | 125 |
| 137 msidata_coordinates = cbind(coord(msidata_$i)[,1:2], 1:ncol(msidata_$i)) | 126 msidata_coordinates = cbind(coord(msidata_$i)[,1:2], 1:ncol(msidata_$i)) |
| 138 colnames(msidata_coordinates)[3] = "pixel_index" | 127 colnames(msidata_coordinates)[3] = "pixel_index" |
| 139 | 128 |
| 140 annotation_df = merge(msidata_coordinates, input_annotation, by=c("x", "y"), all.x=TRUE) | 129 annotation_df = merge(msidata_coordinates, input_annotation, by=c("x", "y"), all.x=TRUE) |
| 141 annotation_df_sorted = annotation_df[order(annotation_df\$pixel_index),]## orders pixel according to msidata | 130 annotation_df_sorted = annotation_df[order(annotation_df\$pixel_index),] |
| 142 annotation_df_sorted\$pixel_index = NULL | 131 annotation_df_sorted\$pixel_index = NULL |
| 143 | 132 |
| 144 ## extract columnnames from (last) annotation tabular (for QC plot names) | 133 ## extract columnnames from (last) annotation tabular (for QC plot names) |
| 145 annotation_colnames = colnames(input_annotation) | 134 annotation_colnames = colnames(input_annotation) |
| 146 | 135 |
| 169 | 158 |
| 170 ##################### 5) shift coordinates automatically ####################### | 159 ##################### 5) shift coordinates automatically ####################### |
| 171 | 160 |
| 172 #elif str( $combine_conditional.combine_method ) == 'automatic_combine': | 161 #elif str( $combine_conditional.combine_method ) == 'automatic_combine': |
| 173 | 162 |
| 174 ## use name of Galaxy inputfile as sample annotation | 163 ## use name of Galaxy input file as sample annotation |
| 175 sample_name = character() | 164 sample_name = character() |
| 176 #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier)) | 165 #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier)) |
| 177 | 166 |
| 178 if (ncol(msidata_$i)>0 & nrow(msidata_$i) >0) | 167 if (ncol(msidata_$i)>0 & nrow(msidata_$i) >0) |
| 179 { | 168 { |