# HG changeset patch
# User artbio
# Date 1633307674 0
# Node ID 42ea09d3e693803852b0a9d861489a43b4c6a026
# Parent  c73aa7cc4c4bdb5a497e8382d42a80a575bc39f4
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 9deb533aabc9dc24bb88b98c57e242785142df75"

diff -r c73aa7cc4c4b -r 42ea09d3e693 mutational_patterns.R
--- a/mutational_patterns.R	Sun Oct 03 09:28:32 2021 +0000
+++ b/mutational_patterns.R	Mon Oct 04 00:34:34 2021 +0000
@@ -220,23 +220,23 @@
     pdf(opt$output_cosmic, paper = "special", width = 11.69, height = 11.69)
     pseudo_mut_mat <- mut_mat + 0.0001 # First add a small psuedocount to the mutation count matrix
     if (opt$cosmic_version == "v2") {
-        sp_url <- paste("https://cancer.sanger.ac.uk/cancergenome/assets/", "signatures_probabilities.txt", sep = "")
+        sp_url <- "https://cancer.sanger.ac.uk/signatures/documents/420/COSMIC_v2_SBS_GRCh38.txt"
         cancer_signatures <- read.table(sp_url, sep = "\t", header = TRUE)
-        new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Somatic.Mutation.Type)
+        new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Type)
         cancer_signatures <- cancer_signatures[as.vector(new_order), ]
-        row.names(cancer_signatures) <- cancer_signatures$Somatic.Mutation.Type
-        cancer_signatures <- as.matrix(cancer_signatures[, 4:33])
-        colnames(cancer_signatures) <- gsub("Signature.", "", colnames(cancer_signatures)) # shorten signature labels
+        row.names(cancer_signatures) <- cancer_signatures$Type
+        cancer_signatures <- as.matrix(cancer_signatures[, 2:31])
+        colnames(cancer_signatures) <- gsub("Signature_", "", colnames(cancer_signatures)) # shorten signature labels
         cosmic_tag <- "Signatures (Cosmic v2, March 2015)"
         cosmic_colors <- col_vector[1:30]
         names(cosmic_colors) <- colnames(cancer_signatures)
         } else {
-        sp_url <- "https://raw.githubusercontent.com/ARTbio/startbio/master/sigProfiler_SBS_signatures_2019_05_22.tsv"
+        sp_url <- "https://cancer.sanger.ac.uk/signatures/documents/431/COSMIC_v3_SBS_GRCh38.txt"
         cancer_signatures <- read.table(sp_url, sep = "\t", header = TRUE)
-        new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Somatic.Mutation.Type)
+        new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Type)
         cancer_signatures <- cancer_signatures[as.vector(new_order), ]
-        row.names(cancer_signatures) <- cancer_signatures$Somatic.Mutation.Type
-        cancer_signatures <- as.matrix(cancer_signatures[, 4:70])
+        row.names(cancer_signatures) <- cancer_signatures$Type
+        cancer_signatures <- as.matrix(cancer_signatures[, 2:68])
         colnames(cancer_signatures) <- gsub("SBS", "", colnames(cancer_signatures)) # shorten signature labels
         cosmic_tag <- "Signatures (Cosmic v3, May 2019)"
         cosmic_colors <- col_vector[1:67]
diff -r c73aa7cc4c4b -r 42ea09d3e693 mutational_patterns.xml
--- a/mutational_patterns.xml	Sun Oct 03 09:28:32 2021 +0000
+++ b/mutational_patterns.xml	Mon Oct 04 00:34:34 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy0">
+<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy1">
     <description>from genomic variations in vcf files</description>
     <requirements>
         <requirement type="package" version="3.2.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement>
diff -r c73aa7cc4c4b -r 42ea09d3e693 test-data/cosmic_output1.pdf
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diff -r c73aa7cc4c4b -r 42ea09d3e693 test-data/cosmic_output2.pdf
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diff -r c73aa7cc4c4b -r 42ea09d3e693 test-data/cosmic_output_v3.pdf
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diff -r c73aa7cc4c4b -r 42ea09d3e693 test-data/denovo_1.RData
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diff -r c73aa7cc4c4b -r 42ea09d3e693 test-data/denovo_output1.pdf
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diff -r c73aa7cc4c4b -r 42ea09d3e693 test-data/sig_contrib_table.tsv
--- a/test-data/sig_contrib_table.tsv	Sun Oct 03 09:28:32 2021 +0000
+++ b/test-data/sig_contrib_table.tsv	Mon Oct 04 00:34:34 2021 +0000
@@ -1,5 +1,5 @@
 sample	s1	s2	s3	s4	s5	s6	s7	s8	s9	s10	s11	s12	s13	s14	s15	s16	s17	s18	s19	s20	s21	s22	s23	s24	s25	s26	s27	s28	s29	s30
-ovary-I.vcf	0.11366483685008	0.0109938593266657	0.261053482791866	0	0.102195880307416	0.00220769920517984	0	0.121596331607151	0.0667024002680757	0	0.0463559883343337	0.0477514837858505	0.00153570456409855	0	0.0196723565031216	0.125168078635871	0	0	0	0	0	0	0	0	0.056462960047836	0	0.000124367513387182	0.0245145702590675	0	0
-ovary-H.vcf	0.108363933620392	0.0163896275457592	0.219669872246722	0	0.267579919199733	0	0	0.0644683944374041	0.0647530723986353	0	0.0255690291284295	0	0.0096156971999939	0	0	0.16879742588098	0	0	0	0	0	0	0	0	0.0144022954450145	0	0.00628915179499457	0.0341015811019413	0	0
-lung-G.vcf	0.216042386729494	0.0163285606624902	0.174782553623772	0	0.243519493008331	0	0	0.00859703357366864	0.122147877946073	0	0.031028717517658	0.0398485713623127	0	0	0	0.0426507272713916	0	0	0.0331593375475991	0	0	0	0	0	0.0690376730723399	0	0.00121112083973226	0.00164594684513809	0	0
-lung-F.vcf	0.277447721812717	0.00581547878718051	0.177348626019748	0	0.1009356992577	0	0	0.0920458551898083	0.0183096024827367	0	0.0300240298284301	0.00396441475927008	0	0	0	0.195845126035802	0	0	0	0	0	0	0	0	0.0270963890910293	0	0.0049085436021671	0.041321577314175	0	0.0249369358192356
+ovary-I.vcf	0.107676737465178	0.0107477401085281	0.263118370815298	0	0.0975192598491968	0.00654300960428024	0	0.121325654310372	0.0675812234604709	0	0.0475946682228466	0.0483240788134274	0.00116766365611527	0	0.0195773794486755	0.128367970358363	0	0	0	0	0	0	0	0	0.0564468988265929	0	0.000297382010539655	0.0237119630501146	0	0
+ovary-H.vcf	0.105483533021363	0.0160722050763363	0.220294683323486	0	0.270646531625838	0	0	0.0632630764001629	0.0651960109780565	0	0.0265849338024135	0	0.00937728828228106	0	0	0.169077458531394	0	0	0	0	0	0	0	0	0.0141372418969508	0	0.0064233897483352	0.0334436473133834	0	0
+lung-G.vcf	0.210828794798222	0.0160042182355152	0.174216713183146	0	0.248848735805233	0	0	0.0079146795135654	0.122852241624819	0	0.0316731744534412	0.0400882001887818	0	0	0	0.0415901687752403	0	0	0.0349534584507835	0	0	0	0	0	0.0686079325155911	0	0.0013880107407027	0.00103367171495887	0	0
+lung-F.vcf	0.272200051777229	0.00523782090972898	0.176429226414213	0	0.107322684968036	0	0	0.0922420552015618	0.0176321903825532	0	0.0308049189266778	0.00421945577891649	0	0	0	0.195343895329217	0	0	0	0	0	0	0	0	0.026099693090191	0	0.0050497865751646	0.0410158172026456	0	0.0264024034438657
diff -r c73aa7cc4c4b -r 42ea09d3e693 test-data/sig_contrib_table_v3.tsv
--- a/test-data/sig_contrib_table_v3.tsv	Sun Oct 03 09:28:32 2021 +0000
+++ b/test-data/sig_contrib_table_v3.tsv	Mon Oct 04 00:34:34 2021 +0000
@@ -1,5 +1,5 @@
 sample	s1	s2	s3	s4	s5	s6	s7a	s7b	s7c	s7d	s8	s9	s10a	s10b	s11	s12	s13	s14	s15	s16	s17a	s17b	s18	s19	s20	s21	s22	s23	s24	s25	s26	s27	s28	s29	s30	s31	s32	s33	s34	s35	s36	s37	s38	s39	s40	s41	s42	s43	s44	s45	s46	s47	s48	s49	s50	s51	s52	s53	s54	s55	s56	s57	s58	s59	s60	s84	s85
-ovary-I.vcf	0.0292102144556227	0	0	0.00144007322742414	0	0.0504390788292217	0.00194348408726673	0	0.0525707708741538	0	0.0914724303738797	0	0.000832163233383592	0	0	0	0.00842487825711237	0	0.0135094432679645	0.0366586044772389	0	0	0.0185740536261001	0.00229375063200434	0	0.00970266938170121	0	0	0.00599759333539559	0.0421114673613094	0.0114310779471638	0	0.0135490307866796	0	0.0296793772659665	0.0277524342410843	0.0454269664537971	0.00938724128600892	0.0136144947369238	0	0	0.0833465920869942	0	0.137690178135469	0	0	0	0.00953146514960113	0.0202102619863343	0	0	0	0	4.88486910392704e-05	0.00760389505513268	0.0232276886439185	0	0	0.013878903464201	0	0	0.058642750046278	0.129529443690174	0.000268674913454976	0	0	0
-ovary-H.vcf	0.0523809674402057	0	0	0.0073487755957751	0	0	0.00289534105048845	0	0.028141106223541	0.00357241172591758	0.0900610723552876	0	0.00471257812773401	0	0	0	0.0152354080005807	0	0	0.056026125482423	0	0.00257191790029753	0	0.0165305233542475	0	0.000141899985605957	0	0	0.00488001259024111	0.00918859610852697	0.00475106755263085	0.00663010539344573	0.017109685037444	0	0.04731550745362	0.00365691117000763	0.0328768691449399	0.0120314432988265	0.0167811048132417	0	0	0.0950039544413254	0	0.137196255594851	0	0	0	0	0.0597953621090927	0	0	0	0	4.23604750551013e-05	0.0121309998776711	0.00973226374395621	0	0.00222509583262053	0.0251951439030708	0.0118558225702647	0	0.0846395405044328	0.125310604958315	0.00203316618431609	0	0	0
-lung-G.vcf	0.0873029632099988	0	0	0	0	0.0479104551341112	0.00776867305403075	0	0.0313814579173264	0	0.0609850595672004	0.0172622613117254	0	0.00012666179996385	0	0	0.00765587561722924	0	0	0.0278690467140333	0.000454577309760022	0	0.0206812596225624	0.0359443715017539	0	0.0120875070366763	0.00187879472330278	0	0.00683351257522683	0.0494238708587332	0	0	0	0	0.0480909479022159	0.00328524460204372	0.037243337279276	0.000684746817696913	0.0170460736503824	0	0	0.120242044269861	0	0.0912990485885233	0	0	0.00198825222515588	0	0.00367924369018231	0	0	0.00127107492891469	0	0	0	0.0337265499103692	0	0.00040976068762453	0.035143574313439	0	0	0.080043690949342	0.096390826001613	0	0.00205878889713283	0.0118304473325925	0
-lung-F.vcf	0.130972951527932	0	0.0761687896979774	0	0	0	0	0	0.0340317364900266	0	0.0786848101409268	0	0.00232431375487017	0.00924283426133058	0	0	0	0	0	0.0454990529437777	0	0	0.0111440674145277	0.0156984823484767	0	0.00368064004289289	0.00101383322501298	0	0.00769126266914517	0.0114608643279846	0	0.000168984385199036	0.0236023336834282	0	0.064421387701359	0.00659674935231646	0.036711297327122	0.00568327050616103	0.00956407247236277	0	0	0.0874117950073058	0	0.0752825647107504	0	0	0	0.00313252048097358	0.0213677245928594	0	0	0.0221471177980541	0	0.000825664351643732	0	0.0132117228813227	0	0.00204298080257053	0.0390511638798427	0	0	0.0245617897055234	0.122391156939586	0.00304240662816143	0	0.0111696579485762	0
+ovary-I.vcf	0.0261662312700287	0	0	0.00540922040548445	0	0.0554522494221051	0.0015054005135302	0	0.0527698220499384	0	0.0887078997707257	0	0.000907076161215129	0	0	0	0.00816538925821039	0	0.0128589414347678	0.0380260440755711	0	0	0.0173905924247456	0.001707488229021	0	0.010276473882261	0	0	0.00537132652951311	0.0418328062226971	0.011268103748697	0	0.013513567633232	0	0.0299817999935266	0.0290828169035887	0.0455904351684802	0.00911446107696196	0.0142491074457184	0	0	0.0828680955875177	0	0.137846212289707	0	0	0	0.00955362702540194	0.0176518216878586	0	0	0	0	0	0.00791168443668074	0.023401746173643	0	0	0.0142889494092746	0	0	0.0589804306629367	0.127565493753874	0.00058468535308627	0	0	0
+ovary-H.vcf	0.0514943738497272	0	0	0.0087020810819626	0	0	0.00236410365956529	0	0.0283100865280861	0.00330015778410193	0.0876336183320928	0	0.00461986640013499	0	0	0	0.0149334722781705	0	0	0.0575304849089614	0	0.00251629772375885	0	0.0165652645823303	0	0.000624306444994269	0	0	0.00504372393616242	0.00966085594196363	0.00415555408979927	0.00663515443687386	0.0171493644187634	0	0.0481611871648976	0.00444934777109341	0.0328633359412982	0.0116426528342991	0.0171447988100082	0	0	0.0946683632396481	0	0.137633236641122	0	0	0	0	0.0602320275961475	0	0	0	0	0	0.0124382204627417	0.0101014447648236	0	0.00234093513264533	0.0255780469333522	0.0118621125591813	0	0.0844080841563258	0.123178981782342	0.00205845781262428	0	0	0
+lung-G.vcf	0.0835415571466835	0	0	0	0	0.0531396303027374	0.00733219232339216	0	0.0313762292215084	0	0.0606428164890939	0.0176603522234399	0	0.000123110879620826	0	0	0.00735095968187644	0	0	0.0290566556597906	0.00029875750108526	0	0.0203972540873668	0.0355580201715423	0	0.0123438369843411	0.00148831528108934	0	0.00702152929618746	0.0500581225968108	0	0	0	0	0.0483376674495861	0.00503826980581789	0.0375230365596794	0.000365640786534471	0.0173540188566111	0	0	0.119562508095986	0	0.0922495052872749	0	0	0.00186662484782185	0	0.00198383177758492	0	0	0.0016907139525808	0	0	0	0.0339551728551291	0	0.000506019602171982	0.0354612532013092	0	0	0.0800934470527665	0.0943176689178333	0	0.00204207638725024	0.0102632047174961	0
+lung-F.vcf	0.129733671535086	0	0.0756510632174742	0	0	0	0	0	0.0340346028561247	0	0.0771217892059738	0	0.00227780162121716	0.00924261610588687	0	0	0	0	0	0.0465201871969074	0	0	0.0110305938436319	0.0158255469126101	0	0.00374844346904832	0.00146787555295699	0	0.00847802739839135	0.0105235337001421	0	0.000114895596046716	0.0236577247003424	0	0.0645253165188412	0.00780877511904059	0.0367599879858517	0.00522232526398284	0.0100399736075406	0	0	0.087309725420689	0	0.0759894281641185	0	0	0.000534487830683315	0.00298777004029269	0.0229584360721825	0	0	0.0217298493319228	0	0.00070999042925293	0	0.0141214288614859	0	0.00249376674671315	0.0393307390657661	0	0	0.0241692429399726	0.120513106763722	0.00304686844730181	0	0.0103204084787993	0
diff -r c73aa7cc4c4b -r 42ea09d3e693 test-data/spectrum_output1.pdf
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