Mercurial > repos > recetox > ramclustr
changeset 8:c043e1fd79d1 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4b8a43b863ff8a0ff1d5a08e516068853adf358d
| author | recetox |
|---|---|
| date | Tue, 16 Apr 2024 11:30:05 +0000 |
| parents | 09cabbc3d12d |
| children | d70dd1d6ac4d |
| files | ramclustr.xml ramclustr_wrapper.R test-data/test1_spec_abundance_xcms_1.csv test-data/test1_spec_abundance_xcms_1.tsv test-data/test2_spec_abundance_xcms_2.csv test-data/test2_spec_abundance_xcms_2.tsv test-data/test3_spec_abundance_csv_1.csv test-data/test3_spec_abundance_csv_1.tsv test-data/test4_spec_abundance_csv_2.csv test-data/test4_spec_abundance_csv_2.tsv test-data/test5_spec_abundance.csv test-data/test5_spec_abundance.tsv |
| diffstat | 12 files changed, 52 insertions(+), 52 deletions(-) [+] |
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--- a/ramclustr.xml Thu Oct 12 13:30:54 2023 +0000 +++ b/ramclustr.xml Tue Apr 16 11:30:05 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy3" profile="21.09"> +<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy4" profile="21.09"> <description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description> <macros> <import>macros.xml</import> @@ -153,7 +153,7 @@ </inputs> <outputs> - <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" /> + <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="tsv" /> <expand macro="output_msp"/> </outputs> @@ -175,7 +175,7 @@ <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/> </section> <output name="mass_spectra_merged" file="test1_fill_xcms_1.msp" ftype="msp"/> - <output name="spec_abundance" file="test1_spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/> + <output name="spec_abundance" file="test1_spec_abundance_xcms_1.tsv" ftype="tsv" compare="sim_size" delta="100"/> </test> <test expect_num_outputs="2"><!-- TEST 2 --> <section name="filetype"> @@ -196,7 +196,7 @@ </section> </section> <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="sim_size" delta="100"/> - <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/> + <output name="spec_abundance" file="test2_spec_abundance_xcms_2.tsv" ftype="tsv" compare="sim_size" delta="100"/> </test> <test expect_num_outputs="2"><!-- TEST 3 --> <section name="filetype"> @@ -214,7 +214,7 @@ <param name="mult" value="1"/> </section> <output name="mass_spectra_merged" file="test3_spectra_csv_1.msp" ftype="msp"/> - <output name="spec_abundance" file="test3_spec_abundance_csv_1.csv" ftype="csv"/> + <output name="spec_abundance" file="test3_spec_abundance_csv_1.tsv" ftype="tsv"/> </test> <test expect_num_outputs="2"><!-- TEST 4 --> <section name="filetype">
--- a/ramclustr_wrapper.R Thu Oct 12 13:30:54 2023 +0000 +++ b/ramclustr_wrapper.R Tue Apr 16 11:30:05 2024 +0000 @@ -3,9 +3,9 @@ output_spec_abundance, msp_file) { RAMClustR::write.msp(ramclustr_obj, one.file = output_merge_msp) - write.csv(ramclustr_obj$SpecAbund, + write.table(ramclustr_obj$SpecAbund, file = output_spec_abundance, - row.names = TRUE, quote = FALSE + row.names = TRUE, quote = FALSE, col.names = NA, sep = "\t" ) if (!is.null(msp_file)) {
--- a/test-data/test1_spec_abundance_xcms_1.csv Thu Oct 12 13:30:54 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ 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--- a/test-data/test2_spec_abundance_xcms_2.csv Thu Oct 12 13:30:54 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ 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--- a/test-data/test3_spec_abundance_csv_1.csv Thu Oct 12 13:30:54 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -,C01,C02,C03,C04,C05,C06,C07,C08,C09,C10,C11,C12,C13,C14,C15,C16,C17,C18,C19,C20,C21,C22 -dataset_10908,1143359.6024874,14232152.476587,50449.9418344623,705676.707142857,37132.3539979397,29822.3430533531,48305.5183116056,16320.5463588464,233029.800680246,47298.0528173405,34827.0153828901,24530.3375165206,64864.9659048501,92746.0557178936,398852.491270866,20462.4444316982,315657.07173388,18224.8801651832,119901.384914687,112084.028638642,461198.718995128,10125.6569474277 -dataset_10909,1143359.6024874,14232152.476587,50449.9418344623,705676.707142857,37132.3539979397,29822.3430533531,48305.5183116056,16320.5463588464,233029.800680246,47298.0528173405,34827.0153828901,24530.3375165206,64864.9659048501,92746.0557178936,398852.491270866,20462.4444316982,315657.07173388,18224.8801651832,119901.384914687,112084.028638642,461198.718995128,10125.6569474277 -dataset_10910,1143359.6024874,14232152.476587,50449.9418344623,705676.707142857,37132.3539979397,29822.3430533531,48305.5183116056,16320.5463588464,233029.800680246,47298.0528173405,34827.0153828901,24530.3375165206,64864.9659048501,92746.0557178936,398852.491270866,20462.4444316982,315657.07173388,18224.8801651832,119901.384914687,112084.028638642,461198.718995128,10125.6569474277
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3_spec_abundance_csv_1.tsv Tue Apr 16 11:30:05 2024 +0000 @@ -0,0 +1,4 @@ + C01 C02 C03 C04 C05 C06 C07 C08 C09 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 +dataset_10908 1143359.6024874 14232152.476587 50449.9418344623 705676.707142857 37132.3539979397 29822.3430533531 48305.5183116056 16320.5463588464 233029.800680246 47298.0528173405 34827.0153828901 24530.3375165206 64864.9659048501 92746.0557178936 398852.491270866 20462.4444316982 315657.07173388 18224.8801651832 119901.384914687 112084.028638642 461198.718995128 10125.6569474277 +dataset_10909 1143359.6024874 14232152.476587 50449.9418344623 705676.707142857 37132.3539979397 29822.3430533531 48305.5183116056 16320.5463588464 233029.800680246 47298.0528173405 34827.0153828901 24530.3375165206 64864.9659048501 92746.0557178936 398852.491270866 20462.4444316982 315657.07173388 18224.8801651832 119901.384914687 112084.028638642 461198.718995128 10125.6569474277 +dataset_10910 1143359.6024874 14232152.476587 50449.9418344623 705676.707142857 37132.3539979397 29822.3430533531 48305.5183116056 16320.5463588464 233029.800680246 47298.0528173405 34827.0153828901 24530.3375165206 64864.9659048501 92746.0557178936 398852.491270866 20462.4444316982 315657.07173388 18224.8801651832 119901.384914687 112084.028638642 461198.718995128 10125.6569474277
--- a/test-data/test4_spec_abundance_csv_2.csv Thu Oct 12 13:30:54 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -"","C01","C02","C03","C04","C05","C06","C07","C08","C09","C10","C11","C12","C13","C14","C15","C16","C17","C18","C19","C20","C21","C22","C23","C24","C25","C26","C27","C28","C29","C30","C31","C32","C33","C34","C35","C36","C37","C38" -"dataset_10908",15486747.5366514,705676.707142857,29822.3430533531,224421.528087479,240472.056093119,83802.7176826829,53891.3450571771,46940.0774103402,22283.2365363616,398852.491270866,16487.928248967,1983470.1118411,11998.5253787137,55783.8355817233,185478.847522515,315657.07173388,39349.4112699936,21728.8824232737,32441.4747147792,119901.384914687,461198.718995128,19834.4473795901,43602.3586534436,31889.6464337142,68360.3997127846,21854.49991187,1073398.26666055,156861.055191184,493341.849474475,16176.4044227296,10125.6569474277,37890.4782477985,29454.7192721113,66717.3172710142,4822.46628554095,24485.0599767888,21288.8896720112,103775.906887161 -"dataset_10909",15486747.5366514,705676.707142857,29822.3430533531,224421.528087479,240472.056093119,83802.7176826829,53891.3450571771,46940.0774103402,22283.2365363616,398852.491270866,16487.928248967,1983470.1118411,11998.5253787137,55783.8355817233,185478.847522515,315657.07173388,39349.4112699936,21728.8824232737,32441.4747147792,119901.384914687,461198.718995128,19834.4473795901,43602.3586534436,31889.6464337142,68360.3997127846,21854.49991187,1073398.26666055,156861.055191184,493341.849474475,16176.4044227296,10125.6569474277,37890.4782477985,29454.7192721113,66717.3172710142,4822.46628554095,24485.0599767888,21288.8896720112,103775.906887161 -"dataset_10910",15486747.5366514,705676.707142857,29822.3430533531,224421.528087479,240472.056093119,83802.7176826829,53891.3450571771,46940.0774103402,22283.2365363616,398852.491270866,16487.928248967,1983470.1118411,11998.5253787137,55783.8355817233,185478.847522515,315657.07173388,39349.4112699936,21728.8824232737,32441.4747147792,119901.384914687,461198.718995128,19834.4473795901,43602.3586534436,31889.6464337142,68360.3997127846,21854.49991187,1073398.26666055,156861.055191184,493341.849474475,16176.4044227296,10125.6569474277,37890.4782477985,29454.7192721113,66717.3172710142,4822.46628554095,24485.0599767888,21288.8896720112,103775.906887161
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4_spec_abundance_csv_2.tsv Tue Apr 16 11:30:05 2024 +0000 @@ -0,0 +1,4 @@ +"" "C01" "C02" "C03" "C04" "C05" "C06" "C07" "C08" "C09" "C10" "C11" "C12" "C13" "C14" "C15" "C16" "C17" "C18" "C19" "C20" "C21" "C22" "C23" "C24" "C25" "C26" "C27" "C28" "C29" "C30" "C31" "C32" "C33" "C34" "C35" "C36" "C37" "C38" +"dataset_10908" 15486747.5366514 705676.707142857 29822.3430533531 224421.528087479 240472.056093119 83802.7176826829 53891.3450571771 46940.0774103402 22283.2365363616 398852.491270866 16487.928248967 1983470.1118411 11998.5253787137 55783.8355817233 185478.847522515 315657.07173388 39349.4112699936 21728.8824232737 32441.4747147792 119901.384914687 461198.718995128 19834.4473795901 43602.3586534436 31889.6464337142 68360.3997127846 21854.49991187 1073398.26666055 156861.055191184 493341.849474475 16176.4044227296 10125.6569474277 37890.4782477985 29454.7192721113 66717.3172710142 4822.46628554095 24485.0599767888 21288.8896720112 103775.906887161 +"dataset_10909" 15486747.5366514 705676.707142857 29822.3430533531 224421.528087479 240472.056093119 83802.7176826829 53891.3450571771 46940.0774103402 22283.2365363616 398852.491270866 16487.928248967 1983470.1118411 11998.5253787137 55783.8355817233 185478.847522515 315657.07173388 39349.4112699936 21728.8824232737 32441.4747147792 119901.384914687 461198.718995128 19834.4473795901 43602.3586534436 31889.6464337142 68360.3997127846 21854.49991187 1073398.26666055 156861.055191184 493341.849474475 16176.4044227296 10125.6569474277 37890.4782477985 29454.7192721113 66717.3172710142 4822.46628554095 24485.0599767888 21288.8896720112 103775.906887161 +"dataset_10910" 15486747.5366514 705676.707142857 29822.3430533531 224421.528087479 240472.056093119 83802.7176826829 53891.3450571771 46940.0774103402 22283.2365363616 398852.491270866 16487.928248967 1983470.1118411 11998.5253787137 55783.8355817233 185478.847522515 315657.07173388 39349.4112699936 21728.8824232737 32441.4747147792 119901.384914687 461198.718995128 19834.4473795901 43602.3586534436 31889.6464337142 68360.3997127846 21854.49991187 1073398.26666055 156861.055191184 493341.849474475 16176.4044227296 10125.6569474277 37890.4782477985 29454.7192721113 66717.3172710142 4822.46628554095 24485.0599767888 21288.8896720112 103775.906887161
--- a/test-data/test5_spec_abundance.csv Thu Oct 12 13:30:54 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ 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