| Previous changeset 14:be5d1c3c51e5 (2021-08-29) Next changeset 16:bb6397b94018 (2023-04-19) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441" |
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modified:
data_exporter.xml macros.xml |
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added:
test-data/DGMM_annotations.tabular test-data/coloc1.pdf test-data/coloc2.pdf test-data/coloc3.pdf test-data/coloc_table1.tabular test-data/coloc_table2.tabular test-data/coloc_table3.tabular test-data/dgmm_summary1.tabular test-data/dgmm_summary2.tabular test-data/dgmm_test1.pdf test-data/dgmm_test2.RData test-data/dgmm_test2.pdf test-data/estimates_r1_k6_mz1135.93347167969.tabular test-data/estimates_r2_k10_mz1200.46533203125.tabular test-data/probability_r1_k6_mz1023.70806884766.tabular test-data/probability_r2_k10_mz1135.93347167969.tabular test-data/spatial_DGMM_input.ibd test-data/spatial_DGMM_input.imzML |
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| diff -r be5d1c3c51e5 -r b6a4dd06cde0 data_exporter.xml --- a/data_exporter.xml Sun Aug 29 07:31:38 2021 +0000 +++ b/data_exporter.xml Tue Feb 22 20:57:42 2022 +0000 |
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| @@ -239,7 +239,7 @@ </configfiles> <inputs> <expand macro="reading_msidata"/> - <param name="output_options" type="select" display="checkboxes" optional="False" multiple="true" label="Multiple output files can be selected"> + <param name="output_options" type="select" optional="False" multiple="true" label="Multiple output files can be selected"> <option value="int_matrix" selected="True" >intensity matrix</option> <option value="mz_tabular">mz feature output</option> <option value="pixel_tabular">pixel output</option> @@ -263,7 +263,7 @@ <when value="no_annotation"/> <when value="yes_annotation"> <expand macro="reading_pixel_annotations"/> - <param name="summary_type" type="select" display="checkboxes" optional="False" multiple="true" label="Calculation for each m/z and all pixels of a annotation group" help="This step will only work if pixel annotations are provided"> + <param name="summary_type" type="select" optional="False" multiple="true" label="Calculation for each m/z and all pixels of a annotation group" help="This step will only work if pixel annotations are provided"> <option value="mean">mean</option> <option value="median">median</option> <option value="sd">standard deviation</option> |
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| diff -r be5d1c3c51e5 -r b6a4dd06cde0 macros.xml --- a/macros.xml Sun Aug 29 07:31:38 2021 +0000 +++ b/macros.xml Tue Feb 22 20:57:42 2022 +0000 |
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| @@ -178,7 +178,7 @@ - MSI data: 3 types of input data can be used: - - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_ + - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/imzml/>`_ - Analyze7.5 (upload hdr, img and t2m file via the "composite" function) - Cardinal "MSImageSet" or "MSImagingExperiment" saved as .RData ]]></token> @@ -219,21 +219,21 @@ ]]></token> <token name="@SPECTRA_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ - - Optional file with pixel coordinates and annotation: + - Optional file with pixel coordinates and annotation: - Tabular file: One column with x values, one column with y values and one column with annotations - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes) - Pixel with coordinates outside the coordinates of the input file are ignored + :: - + x_coord y_coord annotation 1 1 healthy 2 1 healthy 3 1 disease ... ... - ]]></token> <xml name="reading_msidata"> |
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| diff -r be5d1c3c51e5 -r b6a4dd06cde0 test-data/DGMM_annotations.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DGMM_annotations.tabular Tue Feb 22 20:57:42 2022 +0000 |
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| @@ -0,0 +1,401 @@ +x y design +1 1 bg +2 1 bg +3 1 circle +4 1 circle +5 1 circle +6 1 circle +7 1 bg +8 1 bg +9 1 bg +10 1 bg +11 1 bg +12 1 bg +13 1 bg +14 1 bg +15 1 bg +16 1 bg +17 1 bg +18 1 bg +19 1 bg +20 1 bg +1 2 circle +2 2 circle +3 2 circle +4 2 circle +5 2 circle +6 2 circle +7 2 circle +8 2 circle +9 2 bg +10 2 bg +11 2 bg +12 2 bg +13 2 bg +14 2 bg +15 2 bg +16 2 bg +17 2 bg +18 2 bg +19 2 bg +20 2 bg +1 3 circle +2 3 circle +3 3 circle +4 3 circle +5 3 circle +6 3 circle +7 3 circle +8 3 circle +9 3 circle +10 3 bg +11 3 bg +12 3 bg +13 3 bg +14 3 bg +15 3 bg +16 3 bg +17 3 bg +18 3 bg +19 3 bg +20 3 bg +1 4 circle +2 4 circle +3 4 circle +4 4 circle +5 4 circle +6 4 circle +7 4 circle +8 4 circle +9 4 circle +10 4 bg +11 4 bg +12 4 bg +13 4 bg +14 4 bg +15 4 bg +16 4 bg +17 4 bg +18 4 bg +19 4 bg +20 4 bg +1 5 circle +2 5 circle +3 5 circle +4 5 circle +5 5 circle +6 5 circle +7 5 circle +8 5 circle +9 5 circle +10 5 bg +11 5 bg +12 5 bg +13 5 bg +14 5 bg +15 5 bg +16 5 bg +17 5 bg +18 5 bg +19 5 bg +20 5 bg +1 6 circle +2 6 circle +3 6 circle +4 6 circle +5 6 circle +6 6 circle +7 6 circle +8 6 circle +9 6 circle +10 6 circle +11 6 bg +12 6 bg +13 6 bg +14 6 bg +15 6 bg +16 6 bg +17 6 bg +18 6 bg +19 6 bg +20 6 bg +1 7 circle +2 7 circle +3 7 circle +4 7 circle +5 7 circle +6 7 circle +7 7 circle +8 7 circle +9 7 circle +10 7 circle +11 7 bg +12 7 bg +13 7 bg +14 7 bg +15 7 bg +16 7 bg +17 7 bg +18 7 bg +19 7 bg +20 7 bg +1 8 circle +2 8 circle +3 8 circle +4 8 circle +5 8 circle +6 8 circle +7 8 circle +8 8 circle +9 8 circle +10 8 bg +11 8 bg +12 8 bg +13 8 bg +14 8 bg +15 8 bg +16 8 bg +17 8 bg +18 8 bg +19 8 bg +20 8 bg +1 9 circle +2 9 circle +3 9 circle +4 9 circle +5 9 circle +6 9 circle +7 9 circle +8 9 circle +9 9 circle +10 9 bg +11 9 bg +12 9 bg +13 9 bg +14 9 bg +15 9 bg +16 9 bg +17 9 bg +18 9 bg +19 9 bg +20 9 bg +1 10 circle +2 10 circle +3 10 circle +4 10 circle +5 10 circle +6 10 circle +7 10 circle +8 10 circle +9 10 bg +10 10 bg +11 10 bg +12 10 bg +13 10 bg +14 10 bg +15 10 bg +16 10 bg +17 10 bg +18 10 bg +19 10 bg +20 10 bg +1 11 bg +2 11 circle +3 11 circle +4 11 circle +5 11 circle +6 11 circle +7 11 circle +8 11 square +9 11 square +10 11 square +11 11 square +12 11 square +13 11 square +14 11 square +15 11 square +16 11 square +17 11 square +18 11 square +19 11 square +20 11 square +1 12 bg +2 12 bg +3 12 bg +4 12 bg +5 12 bg +6 12 bg +7 12 bg +8 12 square +9 12 square +10 12 square +11 12 square +12 12 square +13 12 square +14 12 square +15 12 square +16 12 square +17 12 square +18 12 square +19 12 square +20 12 square +1 13 bg +2 13 bg +3 13 bg +4 13 bg +5 13 bg +6 13 bg +7 13 bg +8 13 square +9 13 square +10 13 square +11 13 square +12 13 square +13 13 square +14 13 square +15 13 square +16 13 square +17 13 square +18 13 square +19 13 square +20 13 square +1 14 bg +2 14 bg +3 14 bg +4 14 bg +5 14 bg +6 14 bg +7 14 bg +8 14 square +9 14 square +10 14 square +11 14 square +12 14 square +13 14 square +14 14 square +15 14 square +16 14 square +17 14 square +18 14 square +19 14 square +20 14 square +1 15 bg +2 15 bg +3 15 bg +4 15 bg +5 15 bg +6 15 bg +7 15 bg +8 15 square +9 15 square +10 15 square +11 15 square +12 15 square +13 15 square +14 15 square +15 15 square +16 15 square +17 15 square +18 15 square +19 15 square +20 15 square +1 16 bg +2 16 bg +3 16 bg +4 16 bg +5 16 bg +6 16 bg +7 16 bg +8 16 square +9 16 square +10 16 square +11 16 square +12 16 square +13 16 square +14 16 square +15 16 square +16 16 square +17 16 square +18 16 square +19 16 square +20 16 square +1 17 bg +2 17 bg +3 17 bg +4 17 bg +5 17 bg +6 17 bg +7 17 bg +8 17 square +9 17 square +10 17 square +11 17 square +12 17 square +13 17 square +14 17 square +15 17 square +16 17 square +17 17 square +18 17 square +19 17 square +20 17 square +1 18 bg +2 18 bg +3 18 bg +4 18 bg +5 18 bg +6 18 bg +7 18 bg +8 18 square +9 18 square +10 18 square +11 18 square +12 18 square +13 18 square +14 18 square +15 18 square +16 18 square +17 18 square +18 18 square +19 18 square +20 18 square +1 19 bg +2 19 bg +3 19 bg +4 19 bg +5 19 bg +6 19 bg +7 19 bg +8 19 square +9 19 square +10 19 square +11 19 square +12 19 square +13 19 square +14 19 square +15 19 square +16 19 square +17 19 square +18 19 square +19 19 square +20 19 square +1 20 bg +2 20 bg +3 20 bg +4 20 bg +5 20 bg +6 20 bg +7 20 bg +8 20 square +9 20 square +10 20 square +11 20 square +12 20 square +13 20 square +14 20 square +15 20 square +16 20 square +17 20 square +18 20 square +19 20 square +20 20 square |
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| diff -r be5d1c3c51e5 -r b6a4dd06cde0 test-data/coloc1.pdf |
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| diff -r be5d1c3c51e5 -r b6a4dd06cde0 test-data/coloc2.pdf |
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| diff -r be5d1c3c51e5 -r b6a4dd06cde0 test-data/coloc3.pdf |
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| diff -r be5d1c3c51e5 -r b6a4dd06cde0 test-data/coloc_table1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coloc_table1.tabular Tue Feb 22 20:57:42 2022 +0000 |
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| @@ -0,0 +1,11 @@ +mz correlation M1 M2 +1023.70806884766 1 1 1 +1135.93347167969 0.94302593356566 0.875 0.875 +1200.46533203125 0.929209321928257 0.865 0.865 +1361.26818847656 0.671211137378556 0.71 0.71 +1227.93798828125 0.667168853181017 0.675 0.675 +1453.50952148438 0.665731065791311 0.695 0.695 +1858.89855957031 0.662094302798731 0.705 0.705 +781.236755371094 0.389123692250897 0.65 0.65 +473.920562744141 0.363240913030914 0.6 0.6 +788.86328125 0.337801573243261 0.605 0.605 |
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| diff -r be5d1c3c51e5 -r b6a4dd06cde0 test-data/coloc_table2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coloc_table2.tabular Tue Feb 22 20:57:42 2022 +0000 |
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| @@ -0,0 +1,6 @@ +mz correlation M1 M2 +473.920562744141 0.894244530237853 1 0.455 +788.86328125 0.767668409422198 1 0.455 +781.236755371094 0.702693174822292 0.989010989010989 0.45 +1135.93347167969 0.41173637823825 0.846153846153846 0.385 +1023.70806884766 0.332982169243747 0.791208791208791 0.36 |
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| diff -r be5d1c3c51e5 -r b6a4dd06cde0 test-data/coloc_table3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coloc_table3.tabular Tue Feb 22 20:57:42 2022 +0000 |
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| @@ -0,0 +1,51 @@ +mz correlation M1 M2 +100.583335876465 1 1 1 +100.666664123535 1 1 1 +100.75 1 1 1 +101.416664123535 1 1 1 +101.916664123535 1 1 1 +102 1 1 1 +102.416664123535 1 1 1 +103 1 1 1 +103.083335876465 1 1 1 +103.5 1 1 1 +103.583335876465 1 1 1 +104.083335876465 1 1 1 +104.583335876465 1 1 1 +104.666664123535 1 1 1 +105.166664123535 1 1 1 +113.5 1 1 0.4 +114.583335876465 1 1 0.666666666666667 +114.666664123535 1 1 0.666666666666667 +119.166664123535 1 1 1 +121.666664123535 1 1 1 +122.166664123535 1 1 1 +122.25 1 1 1 +127.083335876465 1 1 0.666666666666667 +127.166664123535 1 1 0.333333333333333 +127.25 1 1 0.333333333333333 +127.333335876465 1 1 0.4 +127.666664123535 1 1 0.666666666666667 +127.75 1 1 0.333333333333333 +128.25 1 1 0.333333333333333 +128.33332824707 1 1 0.333333333333333 +128.41667175293 1 1 0.4 +134.91667175293 1 1 0.5 +135.58332824707 1 1 0.5 +136.08332824707 1 1 0.5 +138.5 1 1 0.666666666666667 +166.33332824707 1 1 0.4 +166.83332824707 1 1 0.666666666666667 +166.91667175293 1 1 0.5 +167.41667175293 1 1 0.666666666666667 +167.83332824707 1 1 0.333333333333333 +167.91667175293 1 1 0.666666666666667 +168 1 1 1 +168.08332824707 1 1 1 +168.41667175293 1 1 0.5 +168.5 1 1 0.666666666666667 +168.58332824707 1 1 1 +169 1 1 0.666666666666667 +169.08332824707 1 1 1 +169.16667175293 1 1 1 +169.58332824707 1 1 0.666666666666667 |
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| diff -r be5d1c3c51e5 -r b6a4dd06cde0 test-data/dgmm_summary1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dgmm_summary1.tabular Tue Feb 22 20:57:42 2022 +0000 |
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| @@ -0,0 +1,11 @@ +r k Classes/group m/z Feature +1 6 2 473.920562744141 1 +1 6 4 781.236755371094 2 +1 6 1 788.86328125 3 +1 6 3 1023.70806884766 4 +1 6 3 1135.93347167969 5 +1 6 4 1200.46533203125 6 +1 6 2 1227.93798828125 7 +1 6 2 1361.26818847656 8 +1 6 2 1453.50952148438 9 +1 6 2 1858.89855957031 10 |
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| diff -r be5d1c3c51e5 -r b6a4dd06cde0 test-data/dgmm_summary2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dgmm_summary2.tabular Tue Feb 22 20:57:42 2022 +0000 |
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| @@ -0,0 +1,11 @@ +r k Classes/group m/z Feature +2 10 1 473.920562744141 1 +2 10 2 781.236755371094 2 +2 10 1 788.86328125 3 +2 10 1.67 1023.70806884766 4 +2 10 1.67 1135.93347167969 5 +2 10 1.67 1200.46533203125 6 +2 10 1 1227.93798828125 7 +2 10 1.67 1361.26818847656 8 +2 10 1 1453.50952148438 9 +2 10 1.33 1858.89855957031 10 |
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| diff -r be5d1c3c51e5 -r b6a4dd06cde0 test-data/dgmm_test1.pdf |
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| diff -r be5d1c3c51e5 -r b6a4dd06cde0 test-data/estimates_r1_k6_mz1135.93347167969.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/estimates_r1_k6_mz1135.93347167969.tabular Tue Feb 22 20:57:42 2022 +0000 |
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| @@ -0,0 +1,4 @@ +group class mean var +files_ 1 0.172268980321456 0.133976695047921 +files_ 2 4.88607208725277 0.301220362077463 +files_ 3 6.64940193494161 0.752878508867188 |
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| diff -r be5d1c3c51e5 -r b6a4dd06cde0 test-data/estimates_r2_k10_mz1200.46533203125.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/estimates_r2_k10_mz1200.46533203125.tabular Tue Feb 22 20:57:42 2022 +0000 |
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| @@ -0,0 +1,6 @@ +group class mean var +bg 1 0.216553505243044 0.158967083338173 +bg 2 4.13395686852547 0.859771560896229 +circle 3 3.16694802842791 0.372813860593546 +circle 4 4.48944198265987 1.71739690046886 +square 5 3.8928901507304 1.21620428871296 |
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| diff -r be5d1c3c51e5 -r b6a4dd06cde0 test-data/probability_r1_k6_mz1023.70806884766.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/probability_r1_k6_mz1023.70806884766.tabular Tue Feb 22 20:57:42 2022 +0000 |
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| b'@@ -0,0 +1,401 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|
| b |
| diff -r be5d1c3c51e5 -r b6a4dd06cde0 test-data/probability_r2_k10_mz1135.93347167969.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/probability_r2_k10_mz1135.93347167969.tabular Tue Feb 22 20:57:42 2022 +0000 |
| b |
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| diff -r be5d1c3c51e5 -r b6a4dd06cde0 test-data/spatial_DGMM_input.ibd |
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