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comparison colocalization.xml @ 0:d3ca64dafdef draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
author galaxyp
date Tue, 22 Feb 2022 20:52:51 +0000
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-1:000000000000 0:d3ca64dafdef
1 <tool id="cardinal_colocalization" name="MSI colocalization" version="@VERSION@.0">
2 <description>mass spectrometry imaging colocalization</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="2.3">r-gridextra</requirement>
8 </expand>
9 <command detect_errors="exit_code">
10 <![CDATA[
11
12 @INPUT_LINKING@
13 cat '${MSI_colocalization}' &&
14 Rscript '${MSI_colocalization}'
15
16 ]]>
17 </command>
18 <configfiles>
19 <configfile name="MSI_colocalization"><![CDATA[
20
21 ################################# load libraries and read file #################
22
23 library(Cardinal)
24 library(gridExtra)
25
26 @READING_MSIDATA_FULLY_COMPATIBLE@
27
28 #if str($reference_type.reference) == "roi_ref":
29 ## read and extract x,y,annotation information
30 input_tabular <- read.delim("$reference_type.annotation_file", header = $reference_type.tabular_header, stringsAsFactors = FALSE)
31 annotation_input <- input_tabular[,c($reference_type.column_x, $reference_type.column_y, $reference_type.column_names)]
32 annotation_name <- colnames(annotation_input)[3] ##extract header for annotations to later export tabular with same name
33 colnames(annotation_input) <- c("x", "y", "annotation") ## rename annotations header to default name "annotation"
34
35 ## merge with coordinate information of msidata
36 msidata_coordinates <- data.frame(coord(msidata)\$x, coord(msidata)\$y, c(1:ncol(msidata)))
37 colnames(msidata_coordinates) <- c("x", "y", "pixel_index")
38 merged_annotation <- merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE)
39 merged_annotation[is.na(merged_annotation)] <- "NA"
40 merged_annotation <- merged_annotation[order(merged_annotation\$pixel_index),]
41 msidata\$annotation <- as.character(merged_annotation[,4])
42 reference_group <- msidata\$annotation == "$reference_type.ref_name"
43 #end if
44
45 ## remove duplicated coordinates
46 msidata <- msidata[,!duplicated(coord(msidata))]
47
48
49 @DATA_PROPERTIES_INRAM@
50
51
52 ######################################## PDF ###################################
53 ################################################################################
54 ################################################################################
55
56
57 pdf("colocalization.pdf", fonts = "Times", pointsize = 12)
58 plot(0,type='n',axes=FALSE,ann=FALSE)
59
60 title(main=paste0("Colocalization for file: \n\n", "$infile.display_name"))
61
62 grid.table(property_df, rows= NULL)
63
64
65 if (npeaks > 0 && sum(is.na(spectra(msidata)))==0)
66 {
67
68 ## colocalization analysis
69 col_results <- colocalized(msidata,
70 #if str($reference_type.reference) == "mz_ref":
71 mz = $reference_type.mz_value,
72 #else
73 ref = reference_group,
74 #end if
75 n = $n_tophits,
76 sort.by = "$sort_by",
77 threshold = median)
78
79 ## Summary results table
80 col_results_df <- as.data.frame(col_results)
81
82 write.table(col_results_df, file="$coloc_results", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
83
84 ## visualize top 10 m/z features
85
86 if (nrow(col_results_df) <= 10)
87 {
88 for (mass in col_results_df\$mz){
89 par(oma=c(0,0,0,1))## margin for image legend
90 print(image(msidata, mz=mass, plusminus=0.25,
91 main= paste0(round(mass, digits = 2)),
92 contrast.enhance = "histogram", strip=FALSE, ylim= c(maximumy,minimumy)))
93 }
94 }else{
95 for (mass in col_results_df\$mz[1:10]){
96 par(oma=c(0,0,0,1))## margin for image legend
97 print(image(msidata, mz=mass, plusminus=0.25,
98 main= paste0(round(mass, digits = 2)),
99 contrast.enhance = "histogram", strip=FALSE, ylim= c(maximumy,minimumy)))
100 }
101 }
102
103
104 dev.off()
105
106 }else{
107 print("Inputfile has no intensities > 0")
108 }
109
110 ]]></configfile>
111 </configfiles>
112 <inputs>
113 <expand macro="reading_msidata"/>
114 <conditional name="reference_type">
115 <param name="reference" type="select" label="Reference type" help="Region of interest (selected spectra) or m/z feature.">
116 <option value="mz_ref" selected="True">m/z feature</option>
117 <option value="roi_ref">Region of interest (spectra)</option>
118 </param>
119 <when value="mz_ref">
120 <param name="mz_value" type="float" value="1000" label="m/z feature" help="The m/z closest to this m/z value will be used as a reference."/>
121 </when>
122 <when value="roi_ref">
123 <expand macro="reading_pixel_annotations"/>
124 <param name="ref_name" type="text" value="reference" label="Reference name" help="Name has to match exactly on of the annotation names in the annotation file"/>
125 </when>
126 </conditional>
127 <param name="n_tophits" type="integer" value="10" label="Top hits" help="The number of top-ranked colocalized features to return in the tabular file." />
128 <param name="sort_by" type="select" display="radio"
129 label="sort.by" help="The colocalization measure used to rank colocalized features. Possible options
130 include Pearson’s correlation and Manders’ colocalization coefficients.">
131 <option value="correlation" selected="True">Pearson's correlation</option>
132 <option value="M1">Manders' colocalization coefficient 1</option>
133 <option value="M2">Manders' colocalization coefficient 2</option>
134 </param>
135 </inputs>
136 <outputs>
137 <data format="pdf" name="coloc_pdf" from_work_dir="colocalization.pdf" label = "${tool.name} on ${on_string}: results"/>
138 <data format="tabular" name="coloc_results" label="${tool.name} on ${on_string}: summary"/>
139 </outputs>
140 <tests>
141 <test>
142 <param name="infile" value="" ftype="imzml">
143 <composite_data value="spatial_DGMM_input.imzML"/>
144 <composite_data value="spatial_DGMM_input.ibd"/>
145 </param>
146 <conditional name="reference_type">
147 <param name="reference" value="mz_ref"/>
148 <param name="mz_value" value="1000"/>
149 </conditional>
150 <output name="coloc_pdf" file="coloc1.pdf" compare="sim_size" delta="2000"/>
151 <output name="coloc_results" file="coloc_table1.tabular"/>
152 </test>
153 <test>
154 <param name="infile" value="" ftype="imzml">
155 <composite_data value="spatial_DGMM_input.imzML"/>
156 <composite_data value="spatial_DGMM_input.ibd"/>
157 </param>
158 <conditional name="reference_type">
159 <param name="reference" value="roi_ref"/>
160 <param name="annotation_file" value="DGMM_annotations.tabular"/>
161 <param name="column_x" value="1"/>
162 <param name="column_y" value="2"/>
163 <param name="column_names" value="3"/>
164 <param name="tabular_header" value="True"/>
165 <param name="ref_name" value="circle"/>
166 </conditional>
167 <param name="n_tophits" value="5"/>
168 <param name="sort_by" value="M2"/>
169 <output name="coloc_pdf" file="coloc2.pdf" compare="sim_size" delta="2000"/>
170 <output name="coloc_results" file="coloc_table2.tabular"/>
171 </test>
172 <test>
173 <param name="infile" value="123_combined.RData" ftype="rdata"/>
174 <conditional name="reference_type">
175 <param name="reference" value="mz_ref"/>
176 <param name="mz_value" value="102.0"/>
177 </conditional>
178 <param name="n_tophits" value="50"/>
179 <param name="sort_by" value="correlation"/>
180 <output name="coloc_pdf" file="coloc3.pdf" compare="sim_size" delta="2000"/>
181 <output name="coloc_results" file="coloc_table3.tabular"/>
182 </test>
183 </tests>
184 <help>
185 <![CDATA[
186
187 @CARDINAL_DESCRIPTION@
188
189 -----
190
191 This tool finds colocalized features in an imaging dataset. Use it to find m/z features that are colocalized with another m/z feature or regions of interests.
192
193 @MSIDATA_INPUT_DESCRIPTION@
194
195 - NA intensities are not allowed
196 - duplicated coordinates will be removed
197 - it is highly recommended to use a dataset that is reduced for the number of m/z features e.g. pre-processed and optionally filtered for m/z of interest in order to keep computational times reasonable.
198
199
200 **Options**
201
202 - The reference can be either a single m/z feature or a region of interest provided via the annotation file.
203
204 - For single m/z features the closest m/z to the m/z value that is used as reference is used
205 - For regions of interest as a reference the name of the region that should be used as a reference has to be written exactly in the way in which it appears in the annotation file input.
206 @SPECTRA_TABULAR_INPUT_DESCRIPTION@
207
208 - By default, pearson correlation is used to rank the colocalized features. Manders’ colocalization coefficients (M1 and M2) are also provided.
209
210 **Output**
211
212 - Pdf with file info and the ion images of the top 10 m/z features (to plot the ion images for more m/z features use the MSI mz images tool)
213 - Tabular file with the top m/z features and their correlation values (pearson, Manders 1 and Manders 2) with the reference
214
215
216 ]]>
217 </help>
218 <citations>
219 <citation type="doi">10.1093/bioinformatics/btv146</citation>
220 </citations>
221
222 </tool>