Mercurial > repos > bgruening > woundhealing_scratch_assay
changeset 1:6b341a048c2e draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6303638b71a30e15a36550af938ee35e49be560b
| author | bgruening |
|---|---|
| date | Tue, 22 Apr 2025 15:50:15 +0000 |
| parents | 8948cc562b7c |
| children | |
| files | measureWoundClosing.groovy woundhealing.xml |
| diffstat | 2 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/measureWoundClosing.groovy Thu Feb 29 17:43:50 2024 +0000 +++ b/measureWoundClosing.groovy Tue Apr 22 15:50:15 2025 +0000 @@ -181,7 +181,7 @@ rt.save(new File(outputDir, datasetId + ".csv").toString()); // save binned image with ROI binnedImp.setRoi(scratchROI, false) - IJ.save(binnedImp, new File(outputDir, datasetId + ".tif").toString()); + IJ.save(binnedImp, new File(outputDir, datasetId + ".tiff").toString()); } println("Analysis of "+datasetId+" is done!")
--- a/woundhealing.xml Thu Feb 29 17:43:50 2024 +0000 +++ b/woundhealing.xml Tue Apr 22 15:50:15 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="woundhealing_scratch_assay" name="Wound healing scratch assay" version="@VERSION@+galaxy0" profile="23.1"> +<tool id="woundhealing_scratch_assay" name="Wound healing scratch assay" version="@VERSION@+galaxy1" profile="23.1"> <description>image analysis</description> <macros> <import>macros.xml</import> @@ -15,7 +15,7 @@ ln -s '$filename' './input/${filename.element_identifier}' && #end for #end if - ImageJ --ij2 --headless + ImageJ --ij2 --headless --run '$__tool_directory__/measureWoundClosing.groovy' 'inputDir="./input",datasetId="$dataset_id",threshold="$threshold",headless="true",saveResults="true",outDirName="./output"' ]]> @@ -25,7 +25,7 @@ <param name="input_type" type="select" label="Are the input images packed into a tar archive?"> <option value="yes">Yes</option> <option value="no">No</option> - </param> + </param> <when value="no"> <param name="input_images" type="data" multiple="true" format="@FORMATS@" label="Images" /> </when> @@ -37,7 +37,7 @@ <param name="threshold" type="text" label="CoV threshold (-1: auto)" value="-1"/> </inputs> <outputs> - <data name="tif_output" format="tif" from_work_dir="output/*.tif" label="movie output ${on_string}" /> + <data name="tiff_output" format="tiff" from_work_dir="output/*.tiff" label="movie output ${on_string}" /> <data name="csv_output" format="tabular" from_work_dir="output/*.csv" label="tabular output"/> </outputs> <tests> @@ -47,7 +47,7 @@ <param name="input_images" location="https://github.com/sunyi000/wound-healing-htm-screen/raw/main/assets/data/input/A3ROI2_Slow_0000.tif,https://github.com/sunyi000/wound-healing-htm-screen/raw/main/assets/data/input/A3ROI2_Slow_0002.tif" /> </conditional> <param name="dataset_id" value="A3ROI2_Slow" /> - <output name="tif_output" location="https://github.com/sunyi000/wound-healing-htm-screen/raw/main/assets/data/A3ROI2_Slow.tif"/> + <output name="tiff_output" location="https://github.com/sunyi000/wound-healing-htm-screen/raw/main/assets/data/A3ROI2_Slow.tif"/> <output name="csv_output" file="A3ROI2_Slow.csv"/> </test> </tests>