Mercurial > repos > galaxyp > cardinal_mz_images
comparison mz_images.xml @ 18:ae304a72db7b 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 13:42:18 +0000 |
| parents | 5629069fca8f |
| children |
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| 17:80600735685d | 18:ae304a72db7b |
|---|---|
| 1 <tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.0"> | 1 <tool id="cardinal_mz_images" name="MSI mz images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> |
| 2 <description> | 2 <description> |
| 3 mass spectrometry imaging m/z heatmaps | 3 mass spectrometry imaging m/z heatmaps |
| 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="2.3">r-gridextra</requirement> | |
| 10 </expand> | |
| 11 <command detect_errors="aggressive"> | 9 <command detect_errors="aggressive"> |
| 12 <![CDATA[ | 10 <![CDATA[ |
| 13 @INPUT_LINKING@ | 11 @INPUT_LINKING@ |
| 14 cat '${MSI_heatmaps}' && | 12 cat '${MSI_heatmaps}' && |
| 15 Rscript '${MSI_heatmaps}' | 13 Rscript '${MSI_heatmaps}' |
| 81 ## optional svg output with original coordinates | 79 ## optional svg output with original coordinates |
| 82 #if $svg_pixelimage: | 80 #if $svg_pixelimage: |
| 83 print("svg pixel image") | 81 print("svg pixel image") |
| 84 ## reverse y axis for svg output = correct order and nice svg image | 82 ## reverse y axis for svg output = correct order and nice svg image |
| 85 coord(msidata)\$y <- max(coord(msidata)\$y) - coord(msidata)\$y + 1 | 83 coord(msidata)\$y <- max(coord(msidata)\$y) - coord(msidata)\$y + 1 |
| 86 ## works only with MSImageSet as expected | 84 |
| 87 msidata = as(msidata, "MSImageSet") | 85 msidata = as(msidata,"MSImagingExperiment") |
| 88 | 86 |
| 89 svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy) | 87 svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy) |
| 90 par(mar=c(0,0,0,0), oma=c(0,0,0,0))## no margin for svg | 88 par(mar=c(0,0,0,0), oma=c(0,0,0,0))## no margin for svg |
| 91 #if str($light_mode) == "white": | 89 #if str($light_mode) == "white": |
| 92 lightmode() | 90 lightmode() |
| 130 <inputs> | 128 <inputs> |
| 131 <expand macro="reading_msidata"/> | 129 <expand macro="reading_msidata"/> |
| 132 <expand macro="pdf_filename"/> | 130 <expand macro="pdf_filename"/> |
| 133 <expand macro="reading_2_column_mz_tabular"/> | 131 <expand macro="reading_2_column_mz_tabular"/> |
| 134 | 132 |
| 135 <param name="plusminus_dalton" value="0.25" type="float" label="plusminus m/" help="m/z range to add on either side of the given m/z to create a window in which the mean of all intensities will be computed"/> | 133 <param name="plusminus_dalton" value="0.25" type="float" label="plusminus m/z" help="m/z range to add on either side of the given m/z to create a window in which the mean of all intensities will be computed"/> |
| 136 <param name="image_contrast" type="select" label="Contrast enhancement" help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots"> | 134 <param name="image_contrast" type="select" label="Contrast enhancement" help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots"> |
| 137 <option value="none" selected="True">none</option> | 135 <option value="none" selected="True">none</option> |
| 138 <option value="suppression">suppression</option> | 136 <option value="suppression">suppression</option> |
| 139 <option value="histogram">histogram</option> | 137 <option value="histogram">histogram</option> |
| 140 </param> | 138 </param> |
| 191 <data format="svg" name="svg_output" from_work_dir="svg_pixel_output.svg" label="${tool.name} on ${on_string}: image.svg"> | 189 <data format="svg" name="svg_output" from_work_dir="svg_pixel_output.svg" label="${tool.name} on ${on_string}: image.svg"> |
| 192 <filter>svg_pixelimage</filter> | 190 <filter>svg_pixelimage</filter> |
| 193 </data> | 191 </data> |
| 194 </outputs> | 192 </outputs> |
| 195 <tests> | 193 <tests> |
| 196 <test> | 194 <test expect_num_outputs="1"> |
| 197 <expand macro="infile_imzml"/> | 195 <expand macro="infile_imzml"/> |
| 198 <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/> | 196 <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/> |
| 199 <param name="mz_column" value="1"/> | 197 <param name="mz_column" value="1"/> |
| 200 <param name="name_column" value="2"/> | 198 <param name="name_column" value="2"/> |
| 201 <param name="plusminus_dalton" value="0.25"/> | 199 <param name="plusminus_dalton" value="0.25"/> |
| 202 <param name="filename" value="Testfile_imzml"/> | 200 <param name="filename" value="Testfile_imzml"/> |
| 203 <param name="image_contrast" value="histogram"/> | 201 <param name="image_contrast" value="histogram"/> |
| 204 <param name="colorkey" value="True"/> | 202 <param name="colorkey" value="True"/> |
| 205 <output name="plots" file="Heatmaps_imzml.pdf" ftype="pdf" compare="sim_size"/> | 203 <output name="plots" file="Heatmaps_imzml.pdf" ftype="pdf" compare="sim_size"/> |
| 206 </test> | 204 </test> |
| 207 <test> | 205 <test expect_num_outputs="2"> |
| 208 <expand macro="infile_analyze75"/> | 206 <expand macro="infile_analyze75"/> |
| 209 <param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/> | 207 <param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/> |
| 210 <param name="mz_column" value="1"/> | 208 <param name="mz_column" value="1"/> |
| 211 <param name="name_column" value="1"/> | 209 <param name="name_column" value="1"/> |
| 212 <param name="plusminus_dalton" value="0.5"/> | 210 <param name="plusminus_dalton" value="0.5"/> |
| 216 <param name="colorkey" value="True"/> | 214 <param name="colorkey" value="True"/> |
| 217 <param name="svg_pixelimage" value="True"/> | 215 <param name="svg_pixelimage" value="True"/> |
| 218 <output name="plots" file="Heatmaps_analyze75.pdf" ftype="pdf" compare="sim_size"/> | 216 <output name="plots" file="Heatmaps_analyze75.pdf" ftype="pdf" compare="sim_size"/> |
| 219 <output name="svg_output" file="analyze75.svg" ftype="svg" compare="sim_size"/> | 217 <output name="svg_output" file="analyze75.svg" ftype="svg" compare="sim_size"/> |
| 220 </test> | 218 </test> |
| 221 <test> | 219 <test expect_num_outputs="1"> |
| 222 <param name="infile" value="preprocessed.RData" ftype="rdata"/> | 220 <param name="infile" value="preprocessed.RData" ftype="rdata"/> |
| 223 <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/> | 221 <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/> |
| 224 <param name="mz_column" value="1"/> | 222 <param name="mz_column" value="1"/> |
| 225 <param name="name_column" value="2"/> | 223 <param name="name_column" value="2"/> |
| 226 <param name="plusminus_dalton" value="0.5"/> | 224 <param name="plusminus_dalton" value="0.5"/> |
| 227 <param name="colorkey" value="True"/> | 225 <param name="colorkey" value="True"/> |
| 228 <param name="filename" value="Testfile_rdata"/> | 226 <param name="filename" value="Testfile_rdata"/> |
| 229 <output name="plots" file="Heatmaps_rdata.pdf" ftype="pdf" compare="sim_size"/> | 227 <output name="plots" file="Heatmaps_rdata.pdf" ftype="pdf" compare="sim_size"/> |
| 230 </test> | 228 </test> |
| 231 <test> | 229 <test expect_num_outputs="1"> |
| 232 <param name="infile" value="empty_spectra.rdata" ftype="rdata"/> | 230 <param name="infile" value="empty_spectra.rdata" ftype="rdata"/> |
| 233 <param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/> | 231 <param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/> |
| 234 <param name="mz_column" value="1"/> | 232 <param name="mz_column" value="1"/> |
| 235 <param name="name_column" value="1"/> | 233 <param name="name_column" value="1"/> |
| 236 <param name="plusminus_dalton" value="0.5"/> | 234 <param name="plusminus_dalton" value="0.5"/> |
| 237 <param name="colorscale" value="plasma"/> | 235 <param name="colorscale" value="plasma"/> |
| 238 <param name="colorkey" value="False"/> | 236 <param name="colorkey" value="False"/> |
| 239 <param name="filename" value="Testfile_rdata"/> | 237 <param name="filename" value="Testfile_rdata"/> |
| 240 <output name="plots" file="Heatmaps_LM8_file16.pdf" ftype="pdf" compare="sim_size"/> | 238 <output name="plots" file="Heatmaps_LM8_file16.pdf" ftype="pdf" compare="sim_size"/> |
| 241 </test> | 239 </test> |
| 242 <test> | 240 <test expect_num_outputs="1"> |
| 243 <expand macro="processed_infile_imzml"/> | 241 <expand macro="processed_infile_imzml"/> |
| 244 <conditional name="processed_cond"> | 242 <conditional name="processed_cond"> |
| 245 <param name="processed_file" value="processed"/> | 243 <param name="processed_file" value="processed"/> |
| 246 <param name="accuracy" value="200"/> | 244 <param name="accuracy" value="200"/> |
| 247 <param name="units" value="ppm"/> | 245 <param name="units" value="ppm"/> |