Mercurial > repos > galaxyp > cardinal_mz_images
diff 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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--- a/mz_images.xml Wed Apr 19 22:44:58 2023 +0000 +++ b/mz_images.xml Thu Jul 04 13:42:18 2024 +0000 @@ -1,13 +1,11 @@ -<tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.0"> +<tool id="cardinal_mz_images" name="MSI mz images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> <description> mass spectrometry imaging m/z heatmaps </description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - <requirement type="package" version="2.3">r-gridextra</requirement> - </expand> + <expand macro="requirements"/> <command detect_errors="aggressive"> <![CDATA[ @INPUT_LINKING@ @@ -83,8 +81,8 @@ print("svg pixel image") ## reverse y axis for svg output = correct order and nice svg image coord(msidata)\$y <- max(coord(msidata)\$y) - coord(msidata)\$y + 1 - ## works only with MSImageSet as expected - msidata = as(msidata, "MSImageSet") + + msidata = as(msidata,"MSImagingExperiment") 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 @@ -132,7 +130,7 @@ <expand macro="pdf_filename"/> <expand macro="reading_2_column_mz_tabular"/> - <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="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"/> <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> @@ -193,7 +191,7 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <expand macro="infile_imzml"/> <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/> <param name="mz_column" value="1"/> @@ -204,7 +202,7 @@ <param name="colorkey" value="True"/> <output name="plots" file="Heatmaps_imzml.pdf" ftype="pdf" compare="sim_size"/> </test> - <test> + <test expect_num_outputs="2"> <expand macro="infile_analyze75"/> <param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/> <param name="mz_column" value="1"/> @@ -218,7 +216,7 @@ <output name="plots" file="Heatmaps_analyze75.pdf" ftype="pdf" compare="sim_size"/> <output name="svg_output" file="analyze75.svg" ftype="svg" compare="sim_size"/> </test> - <test> + <test expect_num_outputs="1"> <param name="infile" value="preprocessed.RData" ftype="rdata"/> <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/> <param name="mz_column" value="1"/> @@ -228,7 +226,7 @@ <param name="filename" value="Testfile_rdata"/> <output name="plots" file="Heatmaps_rdata.pdf" ftype="pdf" compare="sim_size"/> </test> - <test> + <test expect_num_outputs="1"> <param name="infile" value="empty_spectra.rdata" ftype="rdata"/> <param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/> <param name="mz_column" value="1"/> @@ -239,7 +237,7 @@ <param name="filename" value="Testfile_rdata"/> <output name="plots" file="Heatmaps_LM8_file16.pdf" ftype="pdf" compare="sim_size"/> </test> - <test> + <test expect_num_outputs="1"> <expand macro="processed_infile_imzml"/> <conditional name="processed_cond"> <param name="processed_file" value="processed"/>