Mercurial > repos > artbio > mutational_patterns

changeset 13:6741b819cc15 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 372eb902f528baa8b5465b83d992a1d146343dfe"
author artbio
date Thu, 22 Oct 2020 23:29:28 +0000
parents 7954f0d3517f
children 56c8869a231e
files mutational_patterns.R mutational_patterns.xml test-data/sig_contrib_table.tsv
diffstat 3 files changed, 8 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- 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)
         }
--- 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>
--- 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