# HG changeset patch
# User artbio
# Date 1603409368 0
# Node ID 6741b819cc157b222660629517b76eeffcb231b9
# Parent  7954f0d3517f5ccae61b8b21a1a3f1eec68689d3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 372eb902f528baa8b5465b83d992a1d146343dfe"

diff -r 7954f0d3517f -r 6741b819cc15 mutational_patterns.R
--- a/mutational_patterns.R	Thu Oct 22 21:47:48 2020 +0000
+++ b/mutational_patterns.R	Thu Oct 22 23:29:28 2020 +0000
@@ -354,7 +354,9 @@
         output_table <- t(fit_res$contribution)/rowSums(t(fit_res$contribution))
         colnames(output_table) <- paste0("s", colnames(output_table))
         if (length(levels(factor(levels_table$level))) > 1) {
-            output_table <- data.frame(sample=worklist$sample, output_table)
+            output_table <- data.frame(sample=paste0(metadata_table[metadata_table$element_identifier==colnames(fit_res$contribution),
+                                                                    3], "-", colnames(fit_res$contribution) ),
+                                       output_table)
             } else {
         output_table <- data.frame(sample=rownames(output_table), output_table)
         }
diff -r 7954f0d3517f -r 6741b819cc15 mutational_patterns.xml
--- a/mutational_patterns.xml	Thu Oct 22 21:47:48 2020 +0000
+++ b/mutational_patterns.xml	Thu Oct 22 23:29:28 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy13">
+<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy13.1">
     <description>from genomic variations in vcf files</description>
     <requirements>
         <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement>
diff -r 7954f0d3517f -r 6741b819cc15 test-data/sig_contrib_table.tsv
--- a/test-data/sig_contrib_table.tsv	Thu Oct 22 21:47:48 2020 +0000
+++ b/test-data/sig_contrib_table.tsv	Thu Oct 22 23:29:28 2020 +0000
@@ -1,13 +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
-lung - F.vcf	0.110142906240717	0.0107179228940658	0.250337884546217	0	0.123574305205091	0.00064433123164414	0	0.132427942951795	0.0645286099734586	0	0.0449394465051191	0.0482562813691387	0.0021792135773442	0	0.0208527968750023	0.113202769843279	0	0	0	0	0	0	0	0	0.0534957402074307	0	0	0.0246998485796975	0	0
-lung - F.vcf	0.105077406305297	0.0161426031811577	0.213744671485429	0	0.267847442499011	0	0	0.0744758833337775	0.0589788373729043	0	0.0260566297995198	0.00332317088253305	0.0101947253359771	0	0	0.165596602885273	0	0	0	0	0	0	0	0	0.0157724425494898	0	0.0064649564106814	0.0363246279589487	0	0
-lung - F.vcf	0.211033078587086	0.0166966912787851	0.172186940126079	0	0.286633042356631	0	0	0.00842344130070046	0.11400762247453	0	0.0288922172140213	0.0327352792025852	0	0	0	0.034128625357202	0	0	0.0288565039877324	0	0	0	0	0	0.0631355806535697	0	0.000844012191577089	0.00242696526950036	0	0
-lung - G.vcf	0.275881644071761	0.00660164806875313	0.17426347088712	0	0.102714094410494	0	0	0.0917555941611345	0.0202950075653247	0	0.0296908924905143	0.0090315352239272	0	0	0	0.188940992761965	0	0	0	0	0	0	0	0	0.0273695319074987	0	0.00555599996394483	0.0404508145574958	0	0.0274487739300663
-lung - G.vcf	0.110142906240717	0.0107179228940658	0.250337884546217	0	0.123574305205091	0.00064433123164414	0	0.132427942951795	0.0645286099734586	0	0.0449394465051191	0.0482562813691387	0.0021792135773442	0	0.0208527968750023	0.113202769843279	0	0	0	0	0	0	0	0	0.0534957402074307	0	0	0.0246998485796975	0	0
-lung - G.vcf	0.105077406305297	0.0161426031811577	0.213744671485429	0	0.267847442499011	0	0	0.0744758833337775	0.0589788373729043	0	0.0260566297995198	0.00332317088253305	0.0101947253359771	0	0	0.165596602885273	0	0	0	0	0	0	0	0	0.0157724425494898	0	0.0064649564106814	0.0363246279589487	0	0
-ovary - H.vcf	0.211033078587086	0.0166966912787851	0.172186940126079	0	0.286633042356631	0	0	0.00842344130070046	0.11400762247453	0	0.0288922172140213	0.0327352792025852	0	0	0	0.034128625357202	0	0	0.0288565039877324	0	0	0	0	0	0.0631355806535697	0	0.000844012191577089	0.00242696526950036	0	0
-ovary - H.vcf	0.275881644071761	0.00660164806875313	0.17426347088712	0	0.102714094410494	0	0	0.0917555941611345	0.0202950075653247	0	0.0296908924905143	0.0090315352239272	0	0	0	0.188940992761965	0	0	0	0	0	0	0	0	0.0273695319074987	0	0.00555599996394483	0.0404508145574958	0	0.0274487739300663
-ovary - H.vcf	0.110142906240717	0.0107179228940658	0.250337884546217	0	0.123574305205091	0.00064433123164414	0	0.132427942951795	0.0645286099734586	0	0.0449394465051191	0.0482562813691387	0.0021792135773442	0	0.0208527968750023	0.113202769843279	0	0	0	0	0	0	0	0	0.0534957402074307	0	0	0.0246998485796975	0	0
-ovary - I.vcf	0.105077406305297	0.0161426031811577	0.213744671485429	0	0.267847442499011	0	0	0.0744758833337775	0.0589788373729043	0	0.0260566297995198	0.00332317088253305	0.0101947253359771	0	0	0.165596602885273	0	0	0	0	0	0	0	0	0.0157724425494898	0	0.0064649564106814	0.0363246279589487	0	0
-ovary - I.vcf	0.211033078587086	0.0166966912787851	0.172186940126079	0	0.286633042356631	0	0	0.00842344130070046	0.11400762247453	0	0.0288922172140213	0.0327352792025852	0	0	0	0.034128625357202	0	0	0.0288565039877324	0	0	0	0	0	0.0631355806535697	0	0.000844012191577089	0.00242696526950036	0	0
-ovary - I.vcf	0.275881644071761	0.00660164806875313	0.17426347088712	0	0.102714094410494	0	0	0.0917555941611345	0.0202950075653247	0	0.0296908924905143	0.0090315352239272	0	0	0	0.188940992761965	0	0	0	0	0	0	0	0	0.0273695319074987	0	0.00555599996394483	0.0404508145574958	0	0.0274487739300663
+ovary-I.vcf	0.110142906240717	0.0107179228940658	0.250337884546217	0	0.123574305205091	0.00064433123164414	0	0.132427942951795	0.0645286099734586	0	0.0449394465051191	0.0482562813691387	0.0021792135773442	0	0.0208527968750023	0.113202769843279	0	0	0	0	0	0	0	0	0.0534957402074307	0	0	0.0246998485796975	0	0
+ovary-H.vcf	0.105077406305297	0.0161426031811577	0.213744671485429	0	0.267847442499011	0	0	0.0744758833337775	0.0589788373729043	0	0.0260566297995198	0.00332317088253305	0.0101947253359771	0	0	0.165596602885273	0	0	0	0	0	0	0	0	0.0157724425494898	0	0.0064649564106814	0.0363246279589487	0	0
+lung-G.vcf	0.211033078587086	0.0166966912787851	0.172186940126079	0	0.286633042356631	0	0	0.00842344130070046	0.11400762247453	0	0.0288922172140213	0.0327352792025852	0	0	0	0.034128625357202	0	0	0.0288565039877324	0	0	0	0	0	0.0631355806535697	0	0.000844012191577089	0.00242696526950036	0	0
+lung-F.vcf	0.275881644071761	0.00660164806875313	0.17426347088712	0	0.102714094410494	0	0	0.0917555941611345	0.0202950075653247	0	0.0296908924905143	0.0090315352239272	0	0	0	0.188940992761965	0	0	0	0	0	0	0	0	0.0273695319074987	0	0.00555599996394483	0.0404508145574958	0	0.0274487739300663