| Previous changeset 12:a95a82eb4d50 (2020-10-21) Next changeset 14:59e85306eae5 (2020-12-23) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" |
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modified:
mz_images.xml test-data/Heatmaps_LM8_file16.pdf test-data/Heatmaps_analyze75.pdf test-data/Heatmaps_imzml.pdf test-data/Heatmaps_processed.pdf test-data/Heatmaps_rdata.pdf test-data/centroids_proc.pdf test-data/preprocessing_results1.ibd test-data/preprocessing_results1.imzml test-data/preprocessing_results1.imzml.txt test-data/preprocessing_results1.pdf test-data/preprocessing_results2.ibd test-data/preprocessing_results2.imzml test-data/preprocessing_results2.imzml.txt test-data/preprocessing_results2.pdf test-data/preprocessing_results3.ibd test-data/preprocessing_results3.imzml test-data/preprocessing_results3.imzml.txt test-data/preprocessing_results3.pdf |
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| diff -r a95a82eb4d50 -r a2b57ea6666e mz_images.xml --- a/mz_images.xml Wed Oct 21 22:58:11 2020 +0000 +++ b/mz_images.xml Sun Nov 29 23:23:01 2020 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.1"> +<tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.2"> <description> mass spectrometry imaging m/z heatmaps </description> @@ -62,12 +62,19 @@ ### only plot images when file has features and pixels: par(mar=c(0,0,0,0), oma=c(0,0,0,1))## margin for image legend + +#if str($light_mode) == "white": + lightmode() +#else + darkmode() +#end if + if (ncol(msidata)>0 & nrow(msidata) >0){ if (length(inputmz) != 0){ for (mass in 1:length(inputmz)){ print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, normalize.image="$normalize_image", contrast.enhance = "$image_contrast", - smooth.image = "$image_smoothing", colorkey=$colorkey, colorscale=$colorscale, ylim= c(maximumy,minimumy))) + smooth.image = "$image_smoothing", colorkey=$colorkey, colorscale=$colorscale, alpha.power=$alpha_power, ylim= c(maximumy,minimumy))) title(inputnames[mass], adj = 0.5, line = 1)} @@ -81,7 +88,12 @@ svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy) par(mar=c(0,0,0,0), oma=c(0,0,0,0))## no margin for svg - print(image(msidata, mz = inputmz[1],strip=FALSE, plusminus = $plusminus_dalton, colorscale=$colorscale, colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", normalize.image="$normalize_image")) + #if str($light_mode) == "white": + lightmode() + #else + darkmode() + #end if + print(image(msidata, mz = inputmz[1],strip=FALSE, plusminus = $plusminus_dalton,colorscale=$colorscale, colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", alpha.power=$alpha_power, normalize.image="$normalize_image")) dev.off() #end if @@ -90,15 +102,14 @@ #set $color_string = ','.join(['"%s"' % $color.feature_color for $color in $overlay_cond.colours]) colourvector = c($color_string) - par(mar=c(0,0,0,0), oma=c(0,0,0,1))## margin for image legend print(image(msidata, mz=inputmz, plusminus = $plusminus_dalton, - col=colourvector, + col=colourvector, contrast.enhance = "$image_contrast", normalize.image="$normalize_image", smooth.image = "$image_smoothing", superpose=TRUE, main="overlay of all m/z", - key=FALSE, + key=FALSE, alpha.power=$alpha_power, ylim= c(maximumy,minimumy))) legend("$overlay_cond.legend_position", @@ -121,7 +132,7 @@ <expand macro="pdf_filename"/> <expand macro="reading_2_column_mz_tabular"/> - <param name="plusminus_dalton" value="0.25" type="float" label="m/z range" help="average of the m/z window will be computed"/> + <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"/> <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"> <option value="none" selected="True">none</option> <option value="suppression">suppression</option> @@ -138,6 +149,11 @@ <option value="plasma">plasma</option> <option value="inferno">inferno</option> </param> + <param name="light_mode" type="select" display="radio" label="Image Background"> + <option value="white" selected="True">white</option> + <option value="black">black</option> + </param> + <param name="alpha_power" type="float" value="1" label="Alpha power" help="Opacity scaling factor (1 is linear)"/> <param name="colorkey" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/> <param name="normalize_image" type="boolean" truevalue="linear" falsevalue="none" label="Linear normalization of image"/> <param name="svg_pixelimage" type="boolean" label="Export first valid m/z from tabular file as SVG"/> @@ -233,6 +249,7 @@ <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/> <param name="mz_column" value="1"/> <param name="name_column" value="2"/> + <param name="light_mode" value="black"/> <conditional name="overlay_cond"> <param name="overlay_selection" value="yes_overlay"/> <repeat name="colours"> |
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| diff -r a95a82eb4d50 -r a2b57ea6666e test-data/preprocessing_results1.imzml --- a/test-data/preprocessing_results1.imzml Wed Oct 21 22:58:11 2020 +0000 +++ b/test-data/preprocessing_results1.imzml Sun Nov 29 23:23:01 2020 +0000 |
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| diff -r a95a82eb4d50 -r a2b57ea6666e test-data/preprocessing_results1.imzml.txt --- a/test-data/preprocessing_results1.imzml.txt Wed Oct 21 22:58:11 2020 +0000 +++ b/test-data/preprocessing_results1.imzml.txt Sun Nov 29 23:23:01 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 24 --rw-rw-r-- 1 meli meli 216 Oct 5 19:57 ibd --rw-rw-r-- 1 meli meli 18090 Oct 5 19:57 imzml +-rw-rw-r-- 1 meli meli 336 Nov 29 01:14 ibd +-rw-rw-r-- 1 meli meli 18092 Nov 29 01:14 imzml |
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| diff -r a95a82eb4d50 -r a2b57ea6666e test-data/preprocessing_results2.imzml --- a/test-data/preprocessing_results2.imzml Wed Oct 21 22:58:11 2020 +0000 +++ b/test-data/preprocessing_results2.imzml Sun Nov 29 23:23:01 2020 +0000 |
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| @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="503079b4-538a-4be6-b70d-e52542c66482" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="a597fe6a0184ef339105b3a932f58726a9af549b" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="ebbd9c5a-19a7-4db5-91e0-858065743606" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="471a838ffd01331ad8e6d23a59004e05745bf39c" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| diff -r a95a82eb4d50 -r a2b57ea6666e test-data/preprocessing_results2.imzml.txt --- a/test-data/preprocessing_results2.imzml.txt Wed Oct 21 22:58:11 2020 +0000 +++ b/test-data/preprocessing_results2.imzml.txt Sun Nov 29 23:23:01 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 64 --rw-rw-r-- 1 meli meli 37404 Oct 5 19:57 ibd --rw-rw-r-- 1 meli meli 22796 Oct 5 19:57 imzml +-rw-rw-r-- 1 meli meli 37404 Nov 29 18:03 ibd +-rw-rw-r-- 1 meli meli 22796 Nov 29 18:03 imzml |
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| diff -r a95a82eb4d50 -r a2b57ea6666e test-data/preprocessing_results3.imzml --- a/test-data/preprocessing_results3.imzml Wed Oct 21 22:58:11 2020 +0000 +++ b/test-data/preprocessing_results3.imzml Sun Nov 29 23:23:01 2020 +0000 |
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| diff -r a95a82eb4d50 -r a2b57ea6666e test-data/preprocessing_results3.imzml.txt --- a/test-data/preprocessing_results3.imzml.txt Wed Oct 21 22:58:11 2020 +0000 +++ b/test-data/preprocessing_results3.imzml.txt Sun Nov 29 23:23:01 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 24 --rw-rw-r-- 1 meli meli 960 Oct 5 19:58 ibd --rw-rw-r-- 1 meli meli 18112 Oct 5 19:58 imzml +-rw-rw-r-- 1 meli meli 1456 Nov 29 18:04 ibd +-rw-rw-r-- 1 meli meli 18133 Nov 29 18:04 imzml |
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| diff -r a95a82eb4d50 -r a2b57ea6666e test-data/preprocessing_results3.pdf |
| b |
| Binary file test-data/preprocessing_results3.pdf has changed |