| Previous changeset 27:2e35f925c469 (2022-10-27) Next changeset 29:42b207aaa527 (2022-10-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit be6750cb1d7ae18e71b60ae6f2c55e5331105c4f |
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removed:
elm_networkin_psp_uniprot_lut.tabular kinase_metadata.sql kseaapp_demo.R phosphoelm_kinase_upid_desc.lut run_planemo_test.sh run_r_linter.R shed.yml |
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| diff -r 2e35f925c469 -r 896eb8ae1c8c elm_networkin_psp_uniprot_lut.tabular --- a/elm_networkin_psp_uniprot_lut.tabular Thu Oct 27 18:54:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b"@@ -1,446 +0,0 @@\n-UniProtID\tAccessions\tkinase\tnetworkin_id\tpsp_id\tnetphorest_group\tECs\tgene_names\tDescriptions\n-A9UF07_HUMAN\tA9UF07\tBCR-ABL1 (PSP)\t\tBCR-ABL1\t\t\tBCR/ABL fusion\t2.7.10.2;Non-specific protein-tyrosine kinase\n-AAK1_HUMAN\tQ2M2I8\tAAK1\tAAK1\tAAK1\t\t2.7.11.1\tAAK1;KIAA1048\t2.7.11.1;AP2-associated protein kinase 1;Adaptor-associated kinase 1\n-AAKB1_HUMAN\tQ9Y478\tAMPKB1 (PSP)\t\tAMPKB1\t\t\tPRKAB1;AMPK\t5'-AMP-activated protein kinase subunit beta-1;AMPK subunit beta-1;AMPKb\n-AAKG2_HUMAN\tQ9UGJ0\tAMPKG2 (PSP)\t\tAMPKG2\t\t\tPRKAG2\t5'-AMP-activated protein kinase subunit gamma-2;AMPK gamma2;AMPK subunit gamma-2;H91620p;Isoform C of 5'-AMP-activated protein kinase subunit gamma-2\n-AAPK1_HUMAN\tQ13131\tAMPK_group\tAMPKa1\tAMPKA1\tAMPK_group\t2.7.11.1;2.7.11.26;2.7.11.27;2.7.11.31\tPRKAA1;AMPK1\t2.7.11.1;2.7.11.26;5'-AMP-activated protein kinase catalytic subunit alpha-1;AMPK subunit alpha-1;Acetyl-CoA carboxylase kinase;ACACA kinase;2.7.11.27;Hydroxymethylglutaryl-CoA reductase kinase;HMGCR kinase;2.7.11.31;Tau-protein kinase PRKAA1;Isoform 2 of 5'-AMP-activated protein kinase catalytic subunit alpha-1\n-AAPK2_HUMAN\tP54646\tAMPK_group\tAMPKa2\tAMPKA2\tAMPK_group\t2.7.11.1;2.7.11.27;2.7.11.31\tAMPK;PRKAA2;AMPK2\t2.7.11.1;Acetyl-CoA carboxylase kinase;ACACA kinase;2.7.11.27;Hydroxymethylglutaryl-CoA reductase kinase;HMGCR kinase;2.7.11.31;5'-AMP-activated protein kinase catalytic subunit alpha-2;AMPK subunit alpha-2\n-ABL1_HUMAN\tP00519\tAbl\tAbl\tAbl\tAbl_group\t2.7.10.2\tABL1;ABL;JTK7\t2.7.10.2;Tyrosine-protein kinase ABL1;Abelson murine leukemia viral oncogene homolog 1;Abelson tyrosine-protein kinase 1;Proto-oncogene c-Abl;p150\n-ABL2_HUMAN\tP42684\tAbl2\tAbl2\tArg\tAbl_group\t2.7.10.2\tARG;ABL2;ABLL\tEC 2.7.10.2;Tyrosine-protein kinase ABL2;Abelson murine leukemia viral oncogene homolog 2;Abelson tyrosine-protein kinase 2;Abelson-related gene protein;Tyrosine-protein kinase ARG\n-ACK1_HUMAN\tQ07912\tTNK2\tTNK2\tAck\t\t2.7.10.2;2.7.11.1\tTNK2;ACK1\t2.7.11.1;2.7.10.2;Activated CDC42 kinase 1;ACK-1;Tyrosine kinase non-receptor protein 2\n-ACV1B_HUMAN\tP36896\tALK4 (PSP)\t\tALK4\t\t2.7.11.30\tACVR1B;ACVRLK4;ALK4\tEC 2.7.11.30;Activin receptor type-1B;Activin receptor type IB;ACTR-IB;Activin receptor-like kinase 4;ALK-4;Serine/threonine-protein kinase receptor R2;SKR2;Isoform 5 of Activin receptor type-1B\n-ACVL1_HUMAN\tP37023\tALK1 (PSP)\t\tALK1\t\t2.7.11.30\tACVRL1;ACVRLK1;ALK1\tEC 2.7.11.30;TGF-B superfamily receptor type I;TSR-I;Serine/threonine-protein kinase receptor R3;SKR3;Activin receptor-like kinase 1;ALK-1\n-ADCK5_HUMAN\tQ3MIX3\tADCK5 (PSP)\t\tADCK5\t\t\tADCK5\tUncharacterized aarF domain-containing protein kinase 5;2.7.11.-\n-AKT1_HUMAN\tP31749\tPKBalpha (NetworKIN)\tPKBalpha\tAkt1\tPKB_group\t2.7.11.1\tAKT1;PKB;RAC\t2.7.11.1;PKB;RAC-alpha serine/threonine-protein kinase;Protein kinase B;Protein kinase B alpha;PKB alpha;Proto-oncogene c-Akt;RAC-PK-alpha;Isoform 2 of RAC-alpha serine/threonine-protein kinase\n-AKT2_HUMAN\tP31751\tPKB_beta\tPKBbeta\tAkt2\tPKB_group\t2.7.11.1\tAKT2\tEC 2.7.11.1;RAC-beta serine/threonine-protein kinase;Protein kinase Akt-2;Protein kinase B beta;PKB beta;RAC-PK-beta;Isoform 2 of RAC-beta serine/threonine-protein kinase\n-AKT3_HUMAN\tQ9Y243\tPKB_group\tPKBgamma\tAkt3\tPKB_group\t2.7.11.1\tAKT3;PKBG\tEC 2.7.11.1;RAC-gamma serine/threonine-protein kinase;Protein kinase Akt-3;Protein kinase B gamma;PKB gamma;RAC-PK-gamma;STK-2;Isoform 2 of RAC-gamma serine/threonine-protein kinase\n-ALK_HUMAN\tQ9UM73\tALK\tALK\tALK\t\t2.7.10.1\tALK\t2.7.10.1;ALK tyrosine kinase receptor;Anaplastic lymphoma kinase;CD246\n-ALPK1_HUMAN\tQ96QP1\tAlphaK3 (PSP)\t\tAlphaK3\t\t2.7.11.1\tALPK1;KIAA1527;LAK\t2.7.11.1;Alpha-protein kinase 1;Chromosome 4 kinase;Lymphocyte alpha-protein kinase;Isoform 2 of Alpha-protein kinase 1\n-ALPK3_HUMAN\tQ96L96\tMAK (NetworKIN)\tMAK\t\tRCK_group\t2.7.11.1\tALPK3;KIAA1330;MAK\t2.7.11.1;Alpha-protein kinase 3;Muscle alpha-protein kinase\n-ARAF_HUMAN\tP10398\tARAF (NetworKIN)\tARAF\tARAF\tARAF_BRAF_RAF1_group\t2.7.11.1\tARAF;ARAF1;PKS;PKS2\tEC 2.7.11.1;Serine/threonine-protein kinase A-Raf;Proto-oncogene A-Raf;Proto-oncogene A-R"..b'n kinase;PYT;Isoform 2 of Dual specificity protein kinase TTK\n-TXK_HUMAN\tP42681\tTXK\tTXK\tTXK\tTec_group\t2.7.10.2\tTXK;PTK4;RLK\t2.7.10.2;Tyrosine-protein kinase TXK;Protein-tyrosine kinase 4;Resting lymphocyte kinase\n-TYK2_HUMAN\tP29597\tTyk2\tTyk2\tTyk2\tTyk2\t2.7.10.2\tTYK2\t2.7.10.2;Non-receptor tyrosine-protein kinase TYK2\n-TYRO3_HUMAN\tQ06418\tTyro3 (PSP)\t\tTyro3\t\t2.7.10.1\tTYRO3;BYK;DTK;RSE;SKY;TIF\tEC 2.7.10.1;Tyrosine-protein kinase receptor TYRO3;Tyrosine-protein kinase BYK;Tyrosine-protein kinase DTK;Tyrosine-protein kinase RSE;Tyrosine-protein kinase SKY;Tyrosine-protein kinase TIF\n-UFO_HUMAN\tP30530\tAxl\tAxl\tAXL\t\t2.7.10.1\tAXL;UFO\t2.7.10.1;Tyrosine-protein kinase receptor UFO;AXL oncogene\n-UHMK1_HUMAN\tQ8TAS1\tKIS\tKIS\tKIS\t\t2.7.11.1\tUHMK1;KIS;KIST\tEC 2.7.11.1;Serine/threonine-protein kinase Kist;Kinase interacting with stathmin;PAM COOH-terminal interactor protein 2;P-CIP2;U2AF homology motif kinase 1\n-ULK1_HUMAN\tO75385\tULK1 (PSP)\t\tULK1\t\t2.7.11.1\tULK1;KIAA0722\t2.7.11.1;Serine/threonine-protein kinase ULK1;Autophagy-related protein 1 homolog;ATG1;hATG1;Unc-51-like kinase 1\n-ULK2_HUMAN\tQ8IYT8\tULK2 (PSP)\t\tULK2\t\t2.7.11.1\tULK2;KIAA0623\tEC 2.7.11.1;Serine/threonine-protein kinase ULK2;Unc-51-like kinase 2\n-ULK3_HUMAN\tQ6PHR2\tULK3 (PSP)\t\tULK3\t\t2.7.11.1\tULK3\tEC 2.7.11.1;Serine/threonine-protein kinase ULK3;Unc-51-like kinase 3;Isoform 4 of Serine/threonine-protein kinase ULK3\n-VGFR1_HUMAN\tP17948\tFLT1\tFLT1\tVEGFR1\tKDR_FLT1_group\t2.7.10.1\tFLT1;FLT;FRT;VEGFR1\tEC 2.7.10.1;FLT;Vascular endothelial growth factor receptor 1;VEGFR-1;Fms-like tyrosine kinase 1;FLT-1;Tyrosine-protein kinase FRT;Tyrosine-protein kinase receptor FLT;Vascular permeability factor receptor\n-VGFR2_HUMAN\tP35968\tKDR\tKDR\tVEGFR2\tKDR_FLT1_group\t2.7.10.1\tKDR;FLK1;VEGFR2\t2.7.10.1;Vascular endothelial growth factor receptor 2;VEGFR-2;Fetal liver kinase 1;FLK-1;Kinase insert domain receptor;KDR;Protein-tyrosine kinase receptor flk-1;CD309;Isoform 2 of Vascular endothelial growth factor receptor 2\n-VGFR3_HUMAN\tP35916\tFLT4\tFLT4\t\t\t2.7.10.1\tFLT4;VEGFR3\tEC 2.7.10.1;Vascular endothelial growth factor receptor 3;VEGFR-3;Fms-like tyrosine kinase 4;FLT-4;Tyrosine-protein kinase receptor FLT4\n-VRK1_HUMAN\tQ99986\tVRK1\tVRK1\tVRK1\t\t2.7.11.1\tVRK1\t2.7.11.1;Serine/threonine-protein kinase VRK1;Vaccinia-related kinase 1\n-VRK2_HUMAN\tQ86Y07\tVRK2 (PSP)\t\tVRK2\t\t2.7.11.1\tVRK2\t2.7.11.1;Serine/threonine-protein kinase VRK2;Vaccinia-related kinase 2\n-VRK3_HUMAN\tQ8IV63\tVRK3 (PSP)\t\tVRK3\t\t\tVRK3\tInactive serine/threonine-protein kinase VRK3;Serine/threonine-protein pseudokinase VRK3;Vaccinia-related kinase 3\n-WEE1_HUMAN\tP30291\tWEE1\tWEE1\tWee1\t\t2.7.10.2\tWEE1\tEC 2.7.10.2;Wee1-like protein kinase;WEE1hu;Wee1A kinase\n-WNK1_HUMAN\tQ9H4A3\tWNK1\tWNK1\tWNK1\t\t2.7.11.1\tWNK1;HSN2;KDP;KIAA0344;PRKWNK1\t2.7.11.1;p65;Serine/threonine-protein kinase WNK1;Erythrocyte 65 kDa protein;Kinase deficient protein;Protein kinase lysine-deficient 1;Protein kinase with no lysine 1;hWNK1;Isoform 6 of Serine/threonine-protein kinase WNK1\n-WNK2_HUMAN\tQ9Y3S1\tWNK2 (PSP)\t\tWNK2\t\t2.7.11.1\tWNK2;KIAA1760;P/OKcl.13\t2.7.11.1;Serine/threonine-protein kinase WNK2;Antigen NY-CO-43;Protein kinase lysine-deficient 2;Protein kinase with no lysine 2;Serologically defined colon cancer antigen 43;Isoform 2 of Serine/threonine-protein kinase WNK2\n-WNK3_HUMAN\tQ9BYP7\tWNK3 (PSP)\t\tWNK3\t\t2.7.11.1\tWNK3;KIAA1566;PRKWNK3\t2.7.11.1;Serine/threonine-protein kinase WNK3;Protein kinase lysine-deficient 3;Protein kinase with no lysine 3\n-WNK4_HUMAN\tQ96J92\tWNK4 (PSP)\t\tWNK4\t\t2.7.11.1\tWNK4;PRKWNK4\t2.7.11.1;Serine/threonine-protein kinase WNK4;Protein kinase lysine-deficient 4;Protein kinase with no lysine 4;Isoform 2 of Serine/threonine-protein kinase WNK4\n-YES_HUMAN\tP07947\tYes\tYes\tYes\tSrc_group\t2.7.10.2\tYES1;YES\tEC 2.7.10.2;Tyrosine-protein kinase Yes;Proto-oncogene c-Yes;p61-Yes\n-ZAP70_HUMAN\tP43403\tZAP70\tZAP70\tZAP70\t\t2.7.10.2\tZAP70;SRK\tEC 2.7.10.2;Tyrosine-protein kinase ZAP-70;70 kDa zeta-chain associated protein;Syk-related tyrosine kinase;Isoform 3 of Tyrosine-protein kinase ZAP-70\n' |
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| diff -r 2e35f925c469 -r 896eb8ae1c8c kinase_metadata.sql --- a/kinase_metadata.sql Thu Oct 27 18:54:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,209 +0,0 @@ --- add the 'Phosida' site-type name, probably with id 4 -INSERT INTO site_type(type_name) VALUES ('Phosida') -; --- eliminate the table that's about to be defined -DROP TABLE IF EXISTS site_metadata -; --- define the site_metadata table -CREATE TABLE site_metadata( - id INTEGER PRIMARY KEY -, site_type_id INTEGER REFERENCES site_type(id) -, full TEXT UNIQUE ON CONFLICT IGNORE -, abbrev TEXT -, pattern TEXT -, motif TEXT -) -; --- populate the table with initial values -INSERT INTO site_metadata(full, abbrev, site_type_id) - SELECT DISTINCT kinase_map, kinase_map, site_type_id - FROM ppep_gene_site - ORDER BY kinase_map - ; --- change site_type_id to Phosida where appropriate -WITH phoo(id) AS ( - SELECT id - FROM site_type - WHERE type_name = 'Phosida' -) -UPDATE site_metadata - SET site_type_id = (SELECT id FROM phoo) - WHERE abbrev LIKE '%_Phosida%' - ; --- fix messy prefixes due to compound HPRD/Phosida -WITH src(id, abbrev) AS ( - WITH RECURSIVE split(id, content, last, rest) AS ( - SELECT id, '', '', full - FROM site_metadata - WHERE site_type_id = ( - SELECT id - FROM site_type - WHERE type_name = 'Phosida' - ) - AND abbrev LIKE '%(HPRD)%' - UNION ALL - SELECT - id, - CASE - WHEN last = '&' - THEN - substr(rest, 1, 1) - ELSE - content || substr(rest, 1, 1) - END, - substr(rest, 1, 1), - substr(rest, 2) - FROM split - WHERE rest <> '' - ) - SELECT - id, substr(rest, 2) - FROM - split - WHERE last = '&' - AND rest NOT LIKE '%&%' -) -UPDATE site_metadata - SET abbrev = src.abbrev - FROM src - WHERE src.id = site_metadata.id - AND site_metadata.abbrev LIKE '%_Phosida%' - ; --- parse out abbreviation and pattern for Phosida -WITH phoo(id) AS ( - SELECT id - FROM site_type - WHERE type_name = 'Phosida' -) -UPDATE site_metadata - SET abbrev = substr(abbrev, 1, instr(abbrev,'_Phosida ') - 1), - pattern = substr(abbrev, instr(abbrev,'_Phosida ') + 9) - FROM phoo - WHERE site_type_id = phoo.id - AND abbrev LIKE '%_Phosida%' - ; --- parse out abbreviation and pattern for PhosphoSitePlus -WITH psp(id) AS ( - SELECT id - FROM site_type - WHERE type_name = 'PhosphoSite' -) -UPDATE site_metadata - SET abbrev = substr(abbrev, 1, instr(abbrev,'_PhosphoSite') - 1), - pattern = '' - FROM psp - WHERE site_type_id = psp.id - AND abbrev LIKE '%_PhosphoSite%' - ; --- parse out abbreviation and pattern for NetworKIN -WITH ntwrk(id) AS ( - SELECT id - FROM site_type - WHERE type_name = 'NetworKIN' -) -UPDATE site_metadata - SET abbrev = substr(abbrev, 1, instr(abbrev,'_NetworKIN') - 1), - pattern = '' - FROM ntwrk - WHERE site_type_id = ntwrk.id - AND abbrev LIKE '%_NetworKIN%' - ; --- fix messy prefixes due to compound HPRD/HPRD -WITH src(id, abbrev) AS ( - WITH RECURSIVE split(id, content, last, rest) AS ( - SELECT id, '', '', full - FROM site_metadata - WHERE site_type_id = ( - SELECT id - FROM site_type - WHERE type_name = 'motif' - ) - AND abbrev LIKE '%(HPRD)%' - UNION ALL - SELECT - id, - CASE - WHEN last = '&' - THEN - substr(rest, 1, 1) - ELSE - content || substr(rest, 1, 1) - END, - substr(rest, 1, 1), - substr(rest, 2) - FROM split - WHERE rest <> '' - ) - SELECT - id, substr(rest, 2) - FROM - split - WHERE - last = '&' AND rest NOT LIKE '%&%' -) --- SELECT src.abbrev, site_metadata.* --- FROM src, site_metadata --- WHERE src.id = site_metadata.id --- AND site_metadata.abbrev LIKE '%(HPRD)%(HPRD)%' --- ; -UPDATE site_metadata - SET abbrev = src.abbrev - FROM src - WHERE src.id = site_metadata.id - AND site_metadata.abbrev LIKE '%(HPRD)%(HPRD)%' - ; --- parse out abbreviation and pattern for motif -WITH mtf(id) AS ( - SELECT id - FROM site_type - WHERE type_name = 'motif' -) -UPDATE site_metadata - SET abbrev = substr(abbrev, 1, instr(abbrev,'(HPRD) ') - 1), - pattern = substr(abbrev, instr(abbrev,'(HPRD) ') + 7) - FROM mtf - WHERE site_type_id = mtf.id - AND abbrev LIKE '%(HPRD)%' - ; --- trim off verbosities for motif -WITH mtf(id) AS ( - SELECT id - FROM site_type - WHERE type_name = 'motif' -) -UPDATE site_metadata - SET abbrev = substr(abbrev, 1, instr(abbrev,'substrate') - 1), - motif = 'substrate' - FROM mtf - WHERE site_type_id = mtf.id - AND abbrev LIKE '%substrate%' - ; --- trim off verbosities for motif -WITH mtf(id) AS ( - SELECT id - FROM site_type - WHERE type_name = 'motif' -) -UPDATE site_metadata - SET abbrev = substr(abbrev, 1, instr(abbrev,'domain binding motif') - 1), - motif = 'binding' - FROM mtf - WHERE site_type_id = mtf.id - AND abbrev LIKE '%domain binding motif%' - ; - - - - --- DROP TABLE IF EXISTS ppep_gene_siteref --- ; --- --- CREATE TABLE ppep_gene_siteref( --- ppep_id INTEGER REFERENCES ppep(id) --- , gene_names TEXT --- , site_type_id INTEGER REFERENCES site_type(id) --- , site_metadata_id INTEGER REFERENCES site_metadata(id) --- , PRIMARY KEY (ppep_id, site_metadata_id) ON CONFLICT IGNORE --- ); --- - |
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| diff -r 2e35f925c469 -r 896eb8ae1c8c kseaapp_demo.R --- a/kseaapp_demo.R Thu Oct 27 18:54:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,481 +0,0 @@\n-# KSEAapp demo using SQLite data source\n-library(sqldf) # implies that package RSQLite will be available\n-library(KSEAapp) # implies that package gplots will be available\n-\n-# ref: http://adv-r.had.co.nz/Environments.html\n-# "When creating your own environment, note that you should set its parent\n-# environment to be the empty environment. This ensures you don\'t\n-# accidentally inherit objects from somewhere else."\n-# Caution: this prevents `with(my_env, expr)` from working when `expr`\n-# contains anything from the global environment, even operators!\n-# Hence, `x <- 1; get("x", new_env())` fails by design.\n-new_env <- function() {\n- new.env(parent = emptyenv())\n-}\n-\n-# Adapted from KSEAapp::KSEA.Heatmap to allow specification of output file\n-ksea_heatmap <-\n-function(\n- # the data frame outputs from the KSEA.Scores() function, in list format\n- score_list,\n- # a character vector of all the sample names for heatmap annotation:\n- # - the names must be in the same order as the data in score_list\n- # - please avoid long names, as they may get cropped in the final image\n- sample_labels,\n- # character string of either "p.value" or "FDR" indicating the data column\n- # to use for marking statistically significant scores\n- stats,\n- # a numeric value between 0 and infinity indicating the min. number of\n- # substrates a kinase must have to be included in the heatmap\n- m_cutoff,\n- # a numeric value between 0 and 1 indicating the p-value/FDR cutoff\n- # for indicating significant kinases in the heatmap\n- p_cutoff,\n- # a binary input of TRUE or FALSE, indicating whether or not to perform\n- # hierarchical clustering of the sample columns\n- sample_cluster,\n- # a binary input of TRUE or FALSE, indicating whether or not to export\n- # the bar plot as a .tiff image into the working directory\n- export = FALSE\n-) {\n- filter_m <- function(dataset, m_cutoff) {\n- filtered <- dataset[(dataset$m >= m_cutoff), ]\n- return(filtered)\n- }\n- score_list_m <- lapply(score_list, function(...)\n- filter_m(...,\n- m_cutoff))\n- for (i in seq_len(length(score_list_m))) {\n- names <- colnames(score_list_m[[i]])[c(2:7)]\n- colnames(score_list_m[[i]])[c(2:7)] <-\n- paste(names, i, sep = ".")\n- }\n- master <-\n- Reduce(function(...)\n- merge(..., by = "Kinase.Gene", all = F), score_list_m)\n- #ACE if (is.null(master)) return ("No significant kinase genes found") \n- row.names(master) <- master$Kinase.Gene\n- columns <- as.character(colnames(master))\n- merged_scores <- as.matrix(master[, grep("z.score", columns)])\n- colnames(merged_scores) <- sample_labels\n- merged_stats <- as.matrix(master[, grep(stats, columns)])\n- asterisk <- function(matrix) {\n- new <- data.frame()\n- for (i in seq_len(nrow(matrix))) {\n- for (j in seq_len(ncol(matrix))) {\n- if (matrix[i, j] < p_cutoff) {\n- new[i, j] <- "*"\n- }\n- else {\n- new[i, j] <- ""\n- }\n- }\n- }\n- return(new)\n- }\n- merged_asterisk <- as.matrix(asterisk(merged_stats))\n- create_breaks <- function(merged_scores) {\n- if (min(merged_scores) < -1.6) {\n- breaks_neg <- seq(-1.6, 0, length.out = 30)\n- breaks_neg <-\n- append(seq(min(merged_scores), -1.6, length.out = 10), breaks_neg)\n- breaks_neg <- sort(unique(breaks_neg))\n- }\n- else {\n- breaks_neg <- seq(-1.6, 0, length.out = 30)\n- }\n- if (max(merged_scores) > 1.6) {\n- breaks_pos <- seq(0, 1.6, length.out = 30)\n- breaks_pos <-\n- append(breaks_pos, seq(1.6, max(merged_scores), length.out = 10))\n- breaks_pos <- sort(unique(breaks_pos))\n- }\n- else {\n- breaks_pos <- seq(0, 1.6, length.out = 30)\n- }\n- breaks_all <- unique(append(breaks_neg, breaks_pos))\n- mycol_neg <-\n- gplots::colorpanel(n = length(breaks_neg),\n- low = "blue",\n- high = "white")\n- mycol_pos <-\n- gplots::colorpanel(n = length(break'..b' WHERE contrast = %d\n- ", i_cntrst\n- ),\n- connection = db\n- )\n- #ACE K_S_links <-\n- #ACE KSEA.KS_table(\n- #ACE KSEAapp::KSData,\n- #ACE kseaapp_input,\n- #ACE networkin = TRUE,\n- #ACE networkin_cutoff = 2\n- #ACE )\n- #ACE print(sprintf("contrast = %d", i_cntrst))\n- tryCatch(\n- expr = {\n- main_title <- (\n- sprintf(\n- "Change from treatment %s to treatment %s",\n- contrast_metadata_df[i_cntrst, "b_level"],\n- contrast_metadata_df[i_cntrst, "a_level"]\n- )\n- )\n- sub_title <- (\n- sprintf(\n- "Trt %s = {%s}. Trt %s = {%s}.",\n- contrast_metadata_df[i_cntrst, "b_level"],\n- gsub(\n- pattern = ";",\n- replacement = ", ",\n- x = contrast_metadata_df[i_cntrst, "b_samples"],\n- fixed = TRUE\n- ),\n- contrast_metadata_df[i_cntrst, "a_level"],\n- gsub(\n- pattern = ";",\n- replacement = "",\n- x = contrast_metadata_df[i_cntrst, "a_samples"],\n- fixed = TRUE\n- )\n- )\n- )\n- ksea_barplot(\n- KSEAapp::KSData,\n- kseaapp_input,\n- networkin = TRUE,\n- networkin_cutoff = 2,\n- m_cutoff = 2,\n- p_cutoff = 0.05,\n- export = FALSE,\n- main = main_title,\n- sub = sub_title\n- )\n- },\n- error = function(e) {\n- if (tolower(e$message) == err_na_subscr_df_const) {\n- cat(\n- sprintf("\\nNo scores or plot for contrast \'%s\' because:\\n \'%s\'\\n",\n- contrast_label,\n- "There are too many missing or invalid values."\n- ),\n- file = stdout()\n- )\n- } else {\n- cat(\n- sprintf("\\nNo scores or plot for contrast \'%s\' because:\\n \'%s\'\\n",\n- contrast_label,\n- e$message\n- ),\n- file = stdout()\n- )\n- }\n- }\n- )\n- tryCatch(\n- expr = {\n- ksea_scores <-\n- KSEA.Scores(\n- KSEAapp::KSData,\n- kseaapp_input,\n- NetworKIN = TRUE,\n- NetworKIN.cutoff = 2\n- )\n-\n- if (0 < sum(!is.nan(ksea_scores$FDR))) {\n- next_index <- 1 + next_index\n- rslt$score_list[[next_index]] <- ksea_scores\n- #ACE rslt$usable_contrast_list[[next_index]] <- i_cntrst\n- rslt$name_list[[next_index]] <- contrast_label\n- cat("\\n", rslt$name_list[[next_index]], "\\n")\n- low_fdr_print(next_index)\n- }\n- },\n- error = function(e) str(e)\n- )\n-}\n-if (length(rslt$score_list) > 0) {\n- ksea_heatmap(\n- # the data frame outputs from the KSEA.Scores() function, in list format\n- score_list = rslt$score_list,\n- # a character vector of all the sample names for heatmap annotation:\n- # - the names must be in the same order as the data in score_list\n- # - please avoid long names, as they may get cropped in the final image\n- sample_labels = rslt$name_list,\n- # character string of either "p.value" or "FDR" indicating the data column\n- # to use for marking statistically significant scores\n- stats = c("p.value", "FDR")[2],\n- # a numeric value between 0 and infinity indicating the min. number of\n- # substrates a kinase must have to be included in the heatmap\n- m_cutoff = 1,\n- # a numeric value between 0 and 1 indicating the p-value/FDR cutoff\n- # for indicating significant kinases in the heatmap\n- p_cutoff = 0.05,\n- # a binary input of TRUE or FALSE, indicating whether or not to perform\n- # hierarchical clustering of the sample columns\n- sample_cluster = TRUE,\n- # a binary input of TRUE or FALSE, indicating whether or not to export\n- # the bar plot as a .tiff image into the working directory\n- export = FALSE\n- )\n-}\n-dbDisconnect(db)\n' |
| b |
| diff -r 2e35f925c469 -r 896eb8ae1c8c phosphoelm_kinase_upid_desc.lut --- a/phosphoelm_kinase_upid_desc.lut Thu Oct 27 18:54:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,299 +0,0 @@\n-kinase_name\tuniprot_id\tdescription\n-AAK1\tQ2M2I8\tAP2 associated kinase 1\n-Abl\tP00519\tProto-oncogene tyrosine-protein kinase ABL1\n-Abl2\tP42684\tv-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)\n-Abl_drome\tP00522\tTyrosine-protein kinase Abl\n-Ack_drome\tQ9VZI2\tAck\n-AFK\tP80197\tActin-fragmin kinase (Physarum polycephalum)\n-Akt1_drome\tQ8INB9\tRAC serine/threonine-protein kinase\n-AKT_group_Caeel\t\tSerine/threonine-protein kinase akt group\n-ALK\tQ9UM73\tAnaplastic lymphoma kinase\n-AMPK_group\t\t\n-Atg1_drome\tQ9VU14\tAutophagy-specific gene 1\n-ATM\tQ13315\tAtaxia telangiectasia mutated\n-ATR\tQ13535\tAtaxia telangiectasia and Rad3-related protein (FRAP-related protein 1)\n-Aurora A\tO14965\tSerine/threonine-protein kinase 6 (STK6)\n-Aurora B\tQ96GD4\tSerine/threonine-protein kinase 12 (AURKB)\n-Axl\tP30530\tTyrosine-protein kinase receptor UFO\n-BCKDK\tO14874\tBranched-chain alpha-ketoacid dehydrogenase kinase\n-BLK\tP51451\tB lymphoid tyrosine kinase\n-BMPR1B\tO00238\tbone morphogenetic protein receptor, type IB\n-BMX\tP51813\tBMX non-receptor tyrosine kinase (Etk)\n-Brk\tQ13882\tBreast tumor kinase (PTK6)\n-BRSK1\tQ8TDC3\tBR serine/threonine kinase 1 (SAD1A)\n-BTK\tQ06187\tBruton`s tyrosine kinase (AGMX1) (ATK) (BPK)\n-Caki_drome\tQ24210\tCalcium/calmodulin-dependent protein kinase\n-CaM-KI_alpha\tQ14012\tcalcium/calmodulin-dependent protein kinase I\n-CaM-KI_group\t\t\n-CaM-KII_alpha\tQ9UQM7\tcalcium/calmodulin-dependent protein kinase (CaM kinase) II alpha\n-CaM-KII_delta\tQ13557\tcalcium/calmodulin-dependent protein kinase (CaM kinase) II delta\n-CaMKII_drome\tQ00168\tCalcium/calmodulin-dependent protein kinase type II alpha chain\n-CaM-KII_group\t\t\n-CaM-KIV\tQ16566\tcalcium/calmodulin-dependent protein kinase (CaM kinase) IV\n-CaM-KK_alpha\tQ8N5S9\tcalcium/calmodulin-dependent protein kinase kinase 1, alpha\n-CCDPK\tQ9U5L0\tCa2+/calmodulin-dependent protein kinase II (Suberites domuncula)\n-CDC2_drome\tP23572\tCell division protein kinase 1\n-CDK1\tP06493\tCell division control protein 2 homolog (p34 protein kinase) (Cyclin-dependent kinase 1) GENE=CDC2\n-CDK11\tQ9BWU1\tCell division cycle 2-like 6\n-CDK2\tP24941\tCell division protein kinase 2\n-CDK3\tQ00526\tcyclin-dependent kinase 3\n-CDK4\tP11802\tCell division protein kinase 4 (Cyclin-dependent kinase 4)\n-CDK5\tQ00535\tCell division protein kinase 5 \n-CDK6\tQ00534\tcyclin-dependent kinase 6\n-CDK7\tP50613\tCell division protein kinase 7 (CDK-activating kinase) (TFIIH basal transcription factor complex kinase subunit)\n-CDK9\tP50750\tcyclin-dependent kinase 9 (CDC2-related kinase)\n-CDK_group\t\t\n-CDPK\t\tCalcium-dependent protein kinase ( in plants)\n-Chak1\tQ96QT4\ttransient receptor potential cation channel, subfamily M, member 7\n-CHK1\tO14757\tSerine/threonine-protein kinase Chk1\n-CHK2\tO96017\tCHK2 checkpoint homolog\n-CK1_alpha\tP48729\tcasein kinase 1, alpha 1\n-CK1_delta\tP48730\tcasein kinase 1, delta\n-CK1_epsilon\tP49674\tcasein kinase 1, epsilon\n-CK1_group\t\t\n-CK2_alpha\tP68400\tcasein kinase 2, alpha 1 polypeptide\n-CK2_beta\t\t\n-CK2_group\t\t\n-CK_group_Caeel\t\tCasein kinase group\n-CkI_alpha_drome\tP54367\tCasein kinase I isoform alpha\n-CkII_beta_drome\tP08182\tCasein kinase II subunit beta\n-CkII_group_drome\t\tCasein kinase II group\n-CLK1\tP49759\tCDC-like kinase 1\n-CSF1R\tP07333\tcolony stimulating factor 1 receptor, formerly McDonough feline sarcoma viral (v-fms) oncogene homolog\n-Csk\tP41240\tTyrosine-protein kinase CSK\n-DAPK1\tP53355\tdeath-associated protein kinase 1\n-DAPK2\tQ9UIK4\tdeath-associated protein kinase 2\n-DAPK3\tO43293\tdeath-associated protein kinase 3\n-DAPK_group\t\t\n-DCAMKL1\tO15075\tdoublecortin and CaM kinase-like 1\n-DMPK_group\t\t\n-DNA-PK\tP78527\tDNA-dependent protein kinase catalytic subunit\n-DYRK1A\tQ13627\tdual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A\n-DYRK1B\tQ9Y463\tDual specificity tyrosine-phosphorylation-regulated kinase 1B\n-DYRK2\tQ92630\tdual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2\n-DYRK3\tO43781\tdual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3\n-Eg3 kinase\t\tmember of the KIN1/PAR-1/M'..b'in kinase 1\n-PDGFR_alpha\tP16234\tplatelet-derived growth factor receptor, alpha polypeptide\n-PDGFR_beta\tP09619\tplatelet-derived growth factor receptor, beta polypeptide\n-PDGFR_group\t\t\n-PDHK1\tQ15118\tpyruvate dehydrogenase kinase, isozyme 1\n-PDHK2\tQ15119\tpyruvate dehydrogenase kinase, isozyme 2\n-PDHK3\tQ15120\tpyruvate dehydrogenase kinase, isozyme 3\n-PDHK4\tQ16654\tpyruvate dehydrogenase kinase, isozyme 4\n-PDK-1\tO15530\t3-phosphoinositide dependent protein kinase 1\n-PDK-2\t\t\n-PDKC\t\t\n-PHK_group\t\t\n-PIK3CA\t\t\n-PIK3CB\t\t\n-PIK3CD\t\t\n-PIK3CG\t\t\n-PIM-1\tP11309\tpim-1 oncogene\n-PKA_alpha\tP17612\tprotein kinase, cAMP-dependent, catalytic, alpha\n-Pka-C1_drome\tP12370\tcAMP-dependent protein kinase catalytic subunit\n-PKA_group\t\t\n-PKA_group_drome\t\tcAMP-dependent protein kinase catalytic subunit group\n-PKB_beta\tP31751\tv-akt murine thymoma viral oncogene homolog 2\n-PKB_group\t\t\n-PKC_alpha\tP17252\tProtein kinase C, alpha type\n-PKC_beta\tP05771\tprotein kinase C, beta 1\n-PKC_delta\tQ05655\tProtein kinase C, delta type\n-PKC_epsilon\tQ02156\tProtein kinase C, epsilon type\n-PKC_eta\tP24723\tProtein kinase C, eta\n-PKC_gamma\tP05129\tprotein kinase C, gamma\n-PKC_group\t\t\n-PKC_group_drome\t\tProtein kinase C group\n-PKC_iota\tP41743\tprotein kinase C, iota\n-PKC_theta\tQ04759\tProtein kinase C, theta type\n-PKC_zeta\tQ05513\tProtein kinase C, zeta type\n-PKD1\tQ15139\tprotein kinase D1\n-PKD2\tQ9BZL6\tprotein kinase D2\n-PKG1/cGK-I\tP14619\tcGMP-dependent protein kinase 1\n-PKG2/cGK-II\tQ13237\tcGMP-dependent protein kinase 2\n-PKG/cGK_group\t\t\n-PKN1\tQ16512\tprotein kinase N1\n-PLK1\tP53350\tPolo like kinase 1\n-PLK3\tQ9H4B4\tPolo like kinase 3\n-PRP4\tQ13523\tPRP4 pre-mRNA processing factor 4 homolog (yeast)\n-PYK2\tQ14289\tFocal adhesion kinase 2\n-RAF1\tP04049\tRAF proto-oncogene serine/threonine-protein kinase\n-RET\tP07949\tProto-oncogene tyrosine-protein kinase receptor ret\n-ROCK1\tQ13464\tRho-associated, coiled-coil containing protein kinase 1\n-ROCK2\tO75116\tRho-associated, coiled-coil containing protein kinase 2\n-ROCK_group\t\t\n-RON\tQ04912\tMacrophage-stimulating protein receptor ( Stem cell-derived tyrosine kinase) (Mst1r)\n-RSK-1\tQ15418\tRibosomal protein S6 kinase alpha 1\n-RSK-2\tQ15349\tRibosomal protein S6 kinase alpha 2\n-RSK-3\tP51812\tRibosomal protein S6 kinase alpha 3\n-RSK-5\tO75582\tribosomal protein S6 kinase, 90kDa, polypeptide 5 (MSK1)\n-RSK_group\t\t\n-sgg_drome\tP83101\tPutative glycogen synthase kinase-3 homolog\n-SGK_group\t\t\n-SIK\tP57059\tSNF1-like kinase\n-SRC\tP12931\tProto-oncogene tyrosine-protein kinase Src\n-SRC64B_drome\tP00528\tTyrosine-protein kinase Src64B\n-SRC_group\t\t\n-STLK3\tQ9UEW8\tKnown - Refseq /Serine/threonine-protein kinase 39\n-SYK\tP43405\tTyrosine-protein kinase SYK (Spleen tyrosine kinase).\n-TBK1\tQ9UHD2\tTANK-binding kinase 1\n-TEC\tP42680\tTyrosine-protein kinase Tec\n-TESK1\tQ15569\tDual specificity testis-specific protein kinase 1\n-TESK2\tQ96S53\tDual specificity testis-specific protein kinase 2\n-TGFbR1\tP36897\tTGF-beta receptor type I\n-TGFbR2\tP37173\tTGF-beta receptor type II\n-TIE1\tP35590\ttyrosine kinase with immunoglobulin-like and EGF-like domains 1\n-TIE2\tQ02763\tAngiopoietin-1 receptor precursor (EC 2.7.1.112) (Tyrosine-protein kinase receptor TIE-2) (Tyrosine-protein kinase receptor TEK)\n-Titin kinase\t\t\n-TLK1\tQ9UKI8\ttousled-like kinase 1\n-TNK2\tQ07912\ttyrosine kinase, non-receptor, 2 (p21cdc42Hs, ACK)\n-Tor_drome\tP18475\tTarget of rapamycin\n-TRKA\tP04629\tHigh affinity nerve growth factor receptor\n-TRKB\tQ16620\tBDNF/NT-3 growth factors receptor\n-Tropomyosin kinase\t\tTropomyosin receptor kinase (Gallus gallus)\n-TSSK3\tQ96PN8\ttestis-specific serine kinase 3\n-TTK\tP33981\tTTK protein kinase\n-TXK\tP42681\tSyn= Rlk\n-Tyk2\tP29597\tNon-receptor tyrosine-protein kinase TYK2\n-unc-43_Caeel\tQ9NH60\tCalcium/calmodulin-dependent protein kinase II isoform B\n-VRK1\tQ99986\tvaccinia related kinase 1\n-WEE1\tP30291\tWEE1 homolog (S. pombe)\n-WNK1\tQ9H4A3\tWNK lysine deficient protein kinase 1\n-wts_drome\tQ24590\tSerine/threonine kinase PAK homolog DPAK\n-Yes\tP07947\tProto-oncogene tyrosine-protein kinase Yes\n-ZAP70\tP43403\tTyrosine-protein kinase ZAP-70\n' |
| b |
| diff -r 2e35f925c469 -r 896eb8ae1c8c run_planemo_test.sh --- a/run_planemo_test.sh Thu Oct 27 18:54:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -#!/bin/env bash -WHATTOTEST=$1 - -old_path=$PATH -new_path=`echo $PATH | sed -e "s^/home/rstudio/bin/tinytex:^^"` -export PATH=$new_path - -planemo test --biocontainers --galaxy_root ~/galaxy/thor/planemo_galaxy/galaxyproject-galaxy ${WHATTOTEST:-.} |
| b |
| diff -r 2e35f925c469 -r 896eb8ae1c8c run_r_linter.R --- a/run_r_linter.R Thu Oct 27 18:54:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,15 +0,0 @@ -#!/bin/env Rscript -library(lintr) -linters <- linters_with_defaults( - line_length_linter = NULL, - cyclocomp_linter = NULL, - object_usage_linter = NULL -) -cat("linting MaxQuantProcessingScript.R\n") -lint(filename = "MaxQuantProcessingScript.R", linters = linters) -cat("linting mqppep_anova.R\n") -lint(filename = "mqppep_anova.R", linters = linters) -cat("done linting R scripts\n") -cat("linting mqppep_anova_script.Rmd\n") -lint(filename = "mqppep_anova_script.Rmd", linters = linters) -cat("done linting Rmd scripts\n") |
| b |
| diff -r 2e35f925c469 -r 896eb8ae1c8c shed.yml --- a/shed.yml Thu Oct 27 18:54:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,24 +0,0 @@ -name: mqppep -owner: eschen42 -description: MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA -homepage_url: 'https://github.com/galaxyproteomics/tools-galaxyp/' -long_description: | - Phosphoproteomic Enrichment Pipeline provides tools two tools for processing MaxQuant data for phosphoproteome-enriched samples. - - "MaxQuant Phosphopeptide Preprocessing" (mqppep_preproc) transforms the 'Phospho (STY)Sites.txt' output file that MaxQuant produces for for phosphoproteome-enriched samples to prepare it for ANOVA. - - "MaxQuant Phosphopeptide ANOVA" (mqppep_anova) performs ANOVA on the preprocessed data. -remote_repository_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep -type: unrestricted -categories: -- Proteomics -auto_tool_repositories: - name_template: "{{ tool_id }}" - description_template: "Wrapper for the mqppep suite tool: {{ tool_name }}" -suite: - name: "suite_mqppep" - description: suite for preprocessing, ANOVA, and KSEA of MaxQuant results for phosphoproteomic enrichment - long_description: | - Phosphoproteomic Enrichment Pipeline provides tools for preprocessing - the 'Phospho (ST)Sites.txt' or 'Phospho (Y)Sites.txt' files produced - by MaxQuant and for ANOVA analysis of the preprocessed data. |