| Previous changeset 12:e0669b1854b1 (2020-10-22) Next changeset 14:f1897eb07081 (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:
preprocessing.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 e0669b1854b1 -r 6b36be80febb preprocessing.xml --- a/preprocessing.xml Thu Oct 22 20:38:29 2020 +0000 +++ b/preprocessing.xml Sun Nov 29 23:45:08 2020 +0000 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.1">\n+<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.2">\n <description>\n mass spectrometry imaging preprocessing\n </description>\n@@ -47,7 +47,6 @@\n \n \n ## remove duplicated coordinates, otherwise peak picking and log2 transformation will fail\n-msidata <- msidata[,!duplicated(coord(msidata)[,1:2])] \n \n ## set variable to False\n #set $used_peak_picking = False\n@@ -135,24 +134,29 @@\n print(\'gaussian smoothing\')\n \n msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, sd = $method.methods_conditional.methods_for_smoothing.sd_gaussian)\n+ msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))\n \n #elif str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == \'sgolay\':\n print(\'sgolay smoothing\')\n \n msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, order = $method.methods_conditional.methods_for_smoothing.order_of_filters)\n+ msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))\n \n ## if selected replace negative intensities with zero\n #if $method.methods_conditional.methods_for_smoothing.replace_negatives:\n- spectra(msidata)[spectra(msidata)<0] = 0\n+ ## bring spectra matrix to disk\n+ spectra_df = as.matrix(spectra(msidata))\n+ spectra_df[spectra_df<0] = 0\n+ spectra(msidata) = spectra_df\n #end if\n \n #elif str($method.methods_conditional.methods_for_smoothing.smoothing_method) == \'ma\':\n print(\'moving average smoothing\')\n \n msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, coef = $method.methods_conditional.methods_for_smoothing.coefficients_ma_filter)\n+ msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))\n \n #end if\n- msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))\n \n ############################### QC ###########################\n \n@@ -170,7 +174,7 @@\n ############################### Mz alignment ###########################\n \n #elif str( $method.methods_conditional.preprocessing_method ) == \'mz_alignment\':\n- print(\'M/z alignment\')\n+ print(\'m/z alignment\')\n ## M/z alignment\n \n #if str( $method.methods_conditional.mzalign_ref_type.align_reference_datatype) == \'align_table\':\n@@ -183,7 +187,7 @@\n \n #elif str( $method.methods_conditional.mzalign_ref_type.align_reference_datatype) == \'align_noref\':\n \n- msidata = mzAlign(msidata,tolerance = $method.methods_conditional.alignment_tol, units = "$method.methods_conditional.alignment_units", , quantile = $method.methods_conditional.quantile, span = $method.methods_conditional.span)\n+ msidata = mzAlign(msidata,tolerance = $method.methods_conditional.alignment_tol, units = "$method.methods_conditional.alignment_units", quantile = $method.methods_conditional.quantile, span = $method.methods_conditional.span)\n \n #end if\n \n@@ -332,23 +336,23 @@\n #elif str( $method.methods_conditional.preprocessing_method) == \'Mass_binning\':\n print(\'mass binning\')\n \n- #if str( $method.methods_conditional.mz_range.features_filtering) == \'change_mz_range\':\n-\n- #if str($processed_cond.processed_file) == "processed":\n+ #if str($method.methods_conditional.mz_range.f'..b'Select m/z feature filtering option">\n+ \t<param name="features_filtering" type="select" label="Select m/z options">\n <option value="none" selected="True">none</option>\n <option value="change_mz_range">change m/z range</option>\n+ <option value="bin_to_reference">bin m/z to reference</option>\n </param>\n \t\t\t <when value="none"/>\n \t\t\t <when value="change_mz_range">\n \t\t\t\t<param name="min_mz" type="float" value="1" label="Minimum value for m/z"/>\n \t\t\t\t<param name="max_mz" type="float" value="10000" label="Maximum value for m/z"/>\n \t\t\t </when>\n+\t\t\t <when value="bin_to_reference">\n+\t\t <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features as reference for binning. Only the m/z values from the tabular file will be kept."/>\n+\t </when>\n </conditional>\n </when>\n <when value="Transformation">\n@@ -645,7 +642,6 @@\n </when>\n </conditional>\n </repeat>\n- <param name="imzml_output" type="boolean" label="imzML output in processed format" checked="True" truevalue="proc_format" falsevalue="cont_format"/>\n </inputs>\n <outputs>\n <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"/>\n@@ -666,10 +662,8 @@\n <conditional name="methods_conditional">\n <param name="preprocessing_method" value="Smoothing"/>\n <conditional name="methods_for_smoothing">\n- <param name="smoothing_method" value="gaussian"/>\n- <param name="sd_gaussian" value="4"/>\n+ <param name="smoothing_method" value="sgolay"/>\n </conditional>\n- <param name="window_smoothing" value="9"/>\n </conditional>\n </repeat>\n <repeat name="methods">\n@@ -702,7 +696,6 @@\n </conditional>\n </conditional>\n </repeat>\n- <param name="imzml_output" value="cont_format"/>\n <output name="QC_overview" file="preprocessing_results1.pdf" compare="sim_size"/>\n <output name="outfile_imzml" ftype="imzml" file="preprocessing_results1.imzml.txt" compare="sim_size">\n <extra_files type="file" file="preprocessing_results1.imzml" name="imzml" lines_diff="6"/>\n@@ -727,7 +720,6 @@\n <param name="preprocessing_method" value="Peak_alignment"/>\n </conditional>\n </repeat>\n- <param name="imzml_output" value="cont_format"/>\n <output name="QC_overview" file="preprocessing_results2.pdf" compare="sim_size"/>\n <output name="outfile_imzml" ftype="imzml" file="preprocessing_results2.imzml.txt" compare="sim_size">\n <extra_files type="file" file="preprocessing_results2.imzml" name="imzml" lines_diff="6"/>\n@@ -753,13 +745,11 @@\n <conditional name="methods_for_picking">\n <param name="picking_method" value="mad"/>\n </conditional>\n- <param name="imzml_output" value="proc_format"/>\n </conditional>\n </repeat>\n <repeat name="methods">\n <conditional name="methods_conditional">\n <param name="preprocessing_method" value="Peak_alignment"/>\n- <param name="imzml_output" value="proc_format"/>\n </conditional>\n </repeat>\n <output name="QC_overview" file="preprocessing_results3.pdf" compare="sim_size"/>\n@@ -850,7 +840,7 @@\n \n **Output**\n \n-- MSI data as continuous or processed imzML file\n+- MSI data as continuous imzML file\n - pdf with key values and four random mass spectra after each processing step\n \n ]]>\n' |
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| diff -r e0669b1854b1 -r 6b36be80febb test-data/preprocessing_results1.imzml --- a/test-data/preprocessing_results1.imzml Thu Oct 22 20:38:29 2020 +0000 +++ b/test-data/preprocessing_results1.imzml Sun Nov 29 23:45:08 2020 +0000 |
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| b'@@ -9,8 +9,8 @@\n \t\t<fileContent>\n \t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n \t\t\t<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="07177fdd-3760-4df6-8fe2-53d28b280ae8" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="749fe32c8243da06001cf4643c5ce4f1ef5a98a8" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="22bd3147-231d-4076-b6bd-67c1fa7c6ef3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="831eba0fc850529d1351bcbb1baf779fe0773e1b" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n \t\t</fileContent>\n \t</fileDescription>\n@@ -86,15 +86,15 @@\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="36" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="48" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -115,15 +115,15 @@\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="56" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="80" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -144,15 +144,15 @@\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="exter'..b'upRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="156" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="240" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -289,15 +289,15 @@\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" 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/>\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -318,15 +318,15 @@\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="196" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="304" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n' |
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| diff -r e0669b1854b1 -r 6b36be80febb test-data/preprocessing_results1.imzml.txt --- a/test-data/preprocessing_results1.imzml.txt Thu Oct 22 20:38:29 2020 +0000 +++ b/test-data/preprocessing_results1.imzml.txt Sun Nov 29 23:45:08 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 e0669b1854b1 -r 6b36be80febb test-data/preprocessing_results2.imzml --- a/test-data/preprocessing_results2.imzml Thu Oct 22 20:38:29 2020 +0000 +++ b/test-data/preprocessing_results2.imzml Sun Nov 29 23:45:08 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 e0669b1854b1 -r 6b36be80febb test-data/preprocessing_results2.imzml.txt --- a/test-data/preprocessing_results2.imzml.txt Thu Oct 22 20:38:29 2020 +0000 +++ b/test-data/preprocessing_results2.imzml.txt Sun Nov 29 23:45:08 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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| Binary file test-data/preprocessing_results3.ibd has changed |
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