| Previous changeset 16:34fe699200ce (2018-10-09) Next changeset 18:27fbe73c4279 (2019-02-11) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 |
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modified:
README.rst abims_xcms_fillPeaks.xml lib.r repository_dependencies.xml test-data/faahKO.xset.group2.retcor2.group2.fillPeaks2.variableMetadata.tsv |
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| diff -r 34fe699200ce -r b6b62413936f README.rst --- a/README.rst Tue Oct 09 04:42:22 2018 -0400 +++ b/README.rst Fri Nov 09 15:18:21 2018 -0500 |
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| @@ -2,6 +2,11 @@ Changelog/News -------------- +**Version 3.0.0.2 - 09/11/2018** + +- BUGFIX: issue when the vector at peakidx is too long and is written in a new line during the export of the peaklist + + **Version 3.0.0.1 - 09/10/2018** - IMPROVEMENT: the export of the PeakList is now mandatory |
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| diff -r 34fe699200ce -r b6b62413936f abims_xcms_fillPeaks.xml --- a/abims_xcms_fillPeaks.xml Tue Oct 09 04:42:22 2018 -0400 +++ b/abims_xcms_fillPeaks.xml Fri Nov 09 15:18:21 2018 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="abims_xcms_fillPeaks" name="xcms fillChromPeaks (fillPeaks)" version="@WRAPPER_VERSION@.1"> +<tool id="abims_xcms_fillPeaks" name="xcms fillChromPeaks (fillPeaks)" version="@WRAPPER_VERSION@.2"> <description>Integrate areas of missing peaks</description> @@ -230,6 +230,11 @@ Changelog/News -------------- +**Version 3.0.0.2 - 09/11/2018** + +- BUGFIX: issue when the vector at peakidx is too long and is written in a new line during the export of the peaklist + + **Version 3.0.0.1 - 09/10/2018** - IMPROVEMENT: the export of the PeakList is now mandatory |
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| diff -r 34fe699200ce -r b6b62413936f lib.r --- a/lib.r Tue Oct 09 04:42:22 2018 -0400 +++ b/lib.r Fri Nov 09 15:18:21 2018 -0500 |
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| @@ -198,6 +198,9 @@ variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ) dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero) + # FIX: issue when the vector at peakidx is too long and is written in a new line during the export + variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",") + write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F) write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F) @@ -260,9 +263,9 @@ #Create the sampleMetada dataframe sampleMetadata <- xdata@phenoData@data rownames(sampleMetadata) <- NULL - colnames(sampleMetadata) <- c("sampleMetadata", "class") + colnames(sampleMetadata) <- c("sample_name", "class") - sampleNamesOrigin <- sampleMetadata$sampleMetadata + sampleNamesOrigin <- sampleMetadata$sample_name sampleNamesMakeNames <- make.names(sampleNamesOrigin) if (any(duplicated(sampleNamesMakeNames))) { @@ -280,7 +283,7 @@ } } - sampleMetadata$sampleMetadata <- sampleNamesMakeNames + sampleMetadata$sample_name <- sampleNamesMakeNames #For each sample file, the following actions are done |
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| diff -r 34fe699200ce -r b6b62413936f repository_dependencies.xml --- a/repository_dependencies.xml Tue Oct 09 04:42:22 2018 -0400 +++ b/repository_dependencies.xml Fri Nov 09 15:18:21 2018 -0500 |
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| @@ -1,5 +1,5 @@ -<?xml version="1.0"?> +<?xml version="1.0" ?> <repositories> - <repository changeset_revision="7800ba9a4c1e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="544f6d2329ac" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> -</repositories> + <repository changeset_revision="7800ba9a4c1e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu"/> + <repository changeset_revision="544f6d2329ac" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu"/> +</repositories> \ No newline at end of file |
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| diff -r 34fe699200ce -r b6b62413936f test-data/faahKO.xset.group2.retcor2.group2.fillPeaks2.variableMetadata.tsv --- a/test-data/faahKO.xset.group2.retcor2.group2.fillPeaks2.variableMetadata.tsv Tue Oct 09 04:42:22 2018 -0400 +++ b/test-data/faahKO.xset.group2.retcor2.group2.fillPeaks2.variableMetadata.tsv Fri Nov 09 15:18:21 2018 -0500 |
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| b'@@ -1,357 +1,357 @@\n name\tnamecustom\tmz\tmzmin\tmzmax\trt\trtmin\trtmax\tnpeaks\tKO\tWT\tpeakidx\n-M200T3488\tM200.2T3487.9\t200.199996948242\t200.199996948242\t200.199996948242\t3487.93057473838\t3487.93057473838\t3487.93057473838\t1\t1\t0\tc(1089, 10810)\n+M200T3488\tM200.2T3487.9\t200.199996948242\t200.199996948242\t200.199996948242\t3487.93057473838\t3487.93057473838\t3487.93057473838\t1\t1\t0\t1089,10810\n M200T3544\tM200.2T3544\t200.199996948242\t200.199996948242\t200.199996948242\t3543.97068061107\t3543.97068061107\t3543.97068061107\t1\t0\t1\t5859\n-M200T3882\tM200.2T3881.9\t200.199996948242\t200.199996948242\t200.199996948242\t3881.90389692078\t3881.90389692078\t3881.90389692078\t1\t1\t0\tc(1677, 10811, 12248)\n+M200T3882\tM200.2T3881.9\t200.199996948242\t200.199996948242\t200.199996948242\t3881.90389692078\t3881.90389692078\t3881.90389692078\t1\t1\t0\t1677,10811,12248\n M200T3822\tM200.3T3822.3\t200.300003051758\t200.300003051758\t200.300003051758\t3822.28128580992\t3822.28128580992\t3822.28128580992\t1\t0\t1\t6249\n M200T3184\tM200.2T3184.4\t200.199996948242\t200.199996948242\t200.199996948242\t3184.37136447847\t3184.37136447847\t3184.37136447847\t1\t1\t0\t3054\n-M200T2867\tM200.1T2866.7\t200.100006103516\t200.100006103516\t200.100006103516\t2866.7414142519\t2866.7414142519\t2866.7414142519\t1\t1\t0\tc(2697, 9252, 12249, 13693)\n-M200T3978\tM200.3T3978.3\t200.300003051758\t200.300003051758\t200.300003051758\t3978.28977826224\t3978.28977826224\t3978.28977826224\t1\t0\t1\tc(8804, 9253, 12250)\n-M200T3681\tM200.2T3680.7\t200.199996948242\t200.199996948242\t200.199996948242\t3680.7462381127\t3680.7462381127\t3680.7462381127\t1\t0\t1\tc(6014, 10812, 13694)\n+M200T2867\tM200.1T2866.7\t200.100006103516\t200.100006103516\t200.100006103516\t2866.7414142519\t2866.7414142519\t2866.7414142519\t1\t1\t0\t2697,9252,12249,13693\n+M200T3978\tM200.3T3978.3\t200.300003051758\t200.300003051758\t200.300003051758\t3978.28977826224\t3978.28977826224\t3978.28977826224\t1\t0\t1\t8804,9253,12250\n+M200T3681\tM200.2T3680.7\t200.199996948242\t200.199996948242\t200.199996948242\t3680.7462381127\t3680.7462381127\t3680.7462381127\t1\t0\t1\t6014,10812,13694\n M201T3788\tM200.8T3787.9\t200.800003051758\t200.800003051758\t200.800003051758\t3787.9288861147\t3787.9288861147\t3787.9288861147\t1\t0\t1\t6185\n-M201T3536\tM200.8T3536.3\t200.800003051758\t200.800003051758\t200.800003051758\t3536.32508690196\t3536.32508690196\t3536.32508690196\t1\t1\t0\tc(3594, 13695)\n-M201T4052\tM200.8T4052.2\t200.800003051758\t200.800003051758\t200.800003051758\t4052.17447695121\t4052.17447695121\t4052.17447695121\t1\t0\t1\tc(6585, 9254, 10813, 13696)\n-M201T3276\tM200.9T3275.7\t200.900009155273\t200.900009155273\t200.900009155273\t3275.65396470411\t3275.65396470411\t3275.65396470411\t1\t0\t1\tc(5484, 10814, 13697)\n-M201T3630\tM200.9T3630\t200.900009155273\t200.900009155273\t200.900009155273\t3630.01725751236\t3630.01725751236\t3630.01725751236\t1\t0\t1\tc(8310, 12251)\n+M201T3536\tM200.8T3536.3\t200.800003051758\t200.800003051758\t200.800003051758\t3536.32508690196\t3536.32508690196\t3536.32508690196\t1\t1\t0\t3594,13695\n+M201T4052\tM200.8T4052.2\t200.800003051758\t200.800003051758\t200.800003051758\t4052.17447695121\t4052.17447695121\t4052.17447695121\t1\t0\t1\t6585,9254,10813,13696\n+M201T3276\tM200.9T3275.7\t200.900009155273\t200.900009155273\t200.900009155273\t3275.65396470411\t3275.65396470411\t3275.65396470411\t1\t0\t1\t5484,10814,13697\n+M201T3630\tM200.9T3630\t200.900009155273\t200.900009155273\t200.900009155273\t3630.01725751236\t3630.01725751236\t3630.01725751236\t1\t0\t1\t8310,12251\n M201T2590\tM200.9T2590.4\t200.900009155273\t200.900009155273\t200.900009155273\t2590.41928114403\t2590.41928114403\t2590.41928114403\t1\t1\t0\t2311\n M201T3985\tM201.2T3984.7\t201.199996948242\t201.199996948242\t201.199996948242\t3984.68436009228\t3984.68436009228\t3984.68436009228\t1\t0\t1\t6528\n-M201T3138\tM201.1T3138.3\t201.100006103516\t201.100006103516\t201.100006103516\t3138.33722162086\t3138.33722162086\t3138.33722162086\t1\t1\t0\tc(3007, 9255, 12252, 13698)\n+M201T3138\tM201.1T3138.3\t201.100006103516\t201.100006103516\t201.100006103516\t3138.33722162086\t3138.33722162086\t3138.33722162086\t1\t1\t0\t3007,9255,12252,13698\n M201T3693\tM201.2T3692.9\t201.199996948242\t201.199996948242\t201'..b'4062\t599.400024414062\t599.400024414062\t3815.41745314142\t3815.41745314142\t3815.41745314142\t1\t1\t0\tc(1552, 12245, 13688, 15228)\n-M599T2837\tM599.4T2837.3\t599.400024414062\t599.400024414062\t599.400024414062\t2837.32876796317\t2837.32876796317\t2837.32876796317\t1\t1\t0\tc(2616, 10808, 13689)\n-M599T2984\tM599.45T2984.4\t599.450012207031\t599.400024414062\t599.5\t2984.36512439418\t2969.43152576515\t2999.29872302321\t2\t1\t1\tc(2885, 7528)\n+M599T2884\tM599.1T2884\t599.100036621094\t599.100036621094\t599.100036621094\t2884.0322651969\t2884.0322651969\t2884.0322651969\t1\t0\t1\t7424,10806,12243,13686\n+M599T4044\tM599.3T4043.7\t599.299987792969\t599.299987792969\t599.299987792969\t4043.74524093865\t4043.74524093865\t4066.10087588419\t3\t1\t1\t1980,6571,6597,12244,15226\n+M599T3927\tM599.3T3927.1\t599.299987792969\t599.200012207031\t599.299987792969\t3927.1105659975\t3927.1105659975\t3973.23317972754\t3\t1\t1\t4253,8717,8748,10807,13687\n+M599T3455\tM599.25T3455.1\t599.25\t599.200012207031\t599.299987792969\t3455.13028638717\t3436.14286573441\t3474.11770703993\t2\t1\t1\t1028,8116\n+M599T3741\tM599.3T3740.9\t599.299987792969\t599.299987792969\t599.400024414062\t3740.91057539316\t3733.31872427639\t3748.72918614711\t3\t1\t1\t1481,6112,6133,15227\n+M599T4124\tM599.35T4123.8\t599.350006103516\t599.299987792969\t599.400024414062\t4123.8352786937\t4122.9412474863\t4124.72930990111\t2\t1\t1\t4466,9058\n+M599T3815\tM599.4T3815.4\t599.400024414062\t599.400024414062\t599.400024414062\t3815.41745314142\t3815.41745314142\t3815.41745314142\t1\t1\t0\t1552,12245,13688,15228\n+M599T2837\tM599.4T2837.3\t599.400024414062\t599.400024414062\t599.400024414062\t2837.32876796317\t2837.32876796317\t2837.32876796317\t1\t1\t0\t2616,10808,13689\n+M599T2984\tM599.45T2984.4\t599.450012207031\t599.400024414062\t599.5\t2984.36512439418\t2969.43152576515\t2999.29872302321\t2\t1\t1\t2885,7528\n M600T3611\tM599.5T3611.3\t599.5\t599.5\t599.5\t3611.27081973131\t3611.27081973131\t3611.27081973131\t1\t0\t1\t8294\n M600T2728\tM599.5T2728.4\t599.5\t599.5\t599.5\t2728.42534632355\t2728.42534632355\t2728.42534632355\t1\t0\t1\t7235\n-M600T3412\tM599.5T3412.5\t599.5\t599.5\t599.5\t3412.49713875326\t3412.49713875326\t3412.49713875326\t1\t1\t0\tc(999, 12246)\n-M600T2595\tM599.85T2594.7\t599.850006103516\t599.799987792969\t599.900024414062\t2594.74502674603\t2557.12926551055\t2601.08568100398\t4\t2\t2\tc(75, 2316, 4673, 7054)\n+M600T3412\tM599.5T3412.5\t599.5\t599.5\t599.5\t3412.49713875326\t3412.49713875326\t3412.49713875326\t1\t1\t0\t999,12246\n+M600T2595\tM599.85T2594.7\t599.850006103516\t599.799987792969\t599.900024414062\t2594.74502674603\t2557.12926551055\t2601.08568100398\t4\t2\t2\t75,2316,4673,7054\n M600T2782\tM599.9T2782.4\t599.900024414062\t599.900024414062\t599.900024414062\t2782.43037673\t2782.43037673\t2782.43037673\t1\t0\t1\t7290\n-M600T3443\tM600T3443.3\t600\t600\t600\t3443.33609503605\t3428.56063072458\t3458.11155934752\t2\t2\t0\tc(1049, 3394)\n-M600T2847\tM600T2846.8\t600\t600\t600\t2846.75746804785\t2846.75746804785\t2846.75746804785\t1\t0\t1\tc(7388, 13690)\n-M600T2963\tM600T2963.2\t600\t600\t600\t2963.21691026891\t2963.21691026891\t2963.21691026891\t1\t1\t0\tc(455, 13691, 15229)\n-M600T3070\tM600T3070\t600\t600\t600\t3069.97823403078\t3069.97823403078\t3069.97823403078\t1\t0\t1\tc(7609, 10809, 13692)\n-M600T3353\tM600T3352.9\t600\t600\t600\t3352.93056227251\t3352.93056227251\t3352.93056227251\t1\t1\t0\tc(903, 15230)\n-M600T3212\tM600T3212.3\t600\t600\t600\t3212.26402887262\t3212.26402887262\t3212.26402887262\t1\t1\t0\tc(705, 12247)\n+M600T3443\tM600T3443.3\t600\t600\t600\t3443.33609503605\t3428.56063072458\t3458.11155934752\t2\t2\t0\t1049,3394\n+M600T2847\tM600T2846.8\t600\t600\t600\t2846.75746804785\t2846.75746804785\t2846.75746804785\t1\t0\t1\t7388,13690\n+M600T2963\tM600T2963.2\t600\t600\t600\t2963.21691026891\t2963.21691026891\t2963.21691026891\t1\t1\t0\t455,13691,15229\n+M600T3070\tM600T3070\t600\t600\t600\t3069.97823403078\t3069.97823403078\t3069.97823403078\t1\t0\t1\t7609,10809,13692\n+M600T3353\tM600T3352.9\t600\t600\t600\t3352.93056227251\t3352.93056227251\t3352.93056227251\t1\t1\t0\t903,15230\n+M600T3212\tM600T3212.3\t600\t600\t600\t3212.26402887262\t3212.26402887262\t3212.26402887262\t1\t1\t0\t705,12247\n M600T2573\tM600T2573.2\t600\t600\t600\t2573.20528114403\t2573.20528114403\t2573.20528114403\t1\t1\t0\t2295\n' |