# HG changeset patch # User greg # Date 1637018074 0 # Node ID 44b84d32883c278de191b0cdcfbcfb37bccbc8fd # Parent cd636b0e4f95a80f0672694952897aaefcdfd871 "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6" diff -r cd636b0e4f95 -r 44b84d32883c macros.xml --- a/macros.xml Tue Sep 21 00:21:36 2021 +0000 +++ b/macros.xml Mon Nov 15 23:14:34 2021 +0000 @@ -9,7 +9,7 @@ numpy - openpyxl + openpyxl pandas diff -r cd636b0e4f95 -r 44b84d32883c test-data/Mbovis-17_avg_mq_json.json --- a/test-data/Mbovis-17_avg_mq_json.json Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -{"name" diff -r cd636b0e4f95 -r 44b84d32883c test-data/Mbovis-17_snps.fasta --- a/test-data/Mbovis-17_snps.fasta Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->01_1787_FL_Zoo_Jaguar_vcf ->02_0585_COA_TX_Fed_vcf ->02_5877_MEX_TX_Fed_vcf ->root diff -r cd636b0e4f95 -r 44b84d32883c test-data/Mbovis-17_snps_json.json --- a/test-data/Mbovis-17_snps_json.json Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -{"columns": diff -r cd636b0e4f95 -r 44b84d32883c test-data/all_vcf.fasta --- a/test-data/all_vcf.fasta Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->SRR1792272_zc ->input_zc ->SRR8073662_zc ->root diff -r cd636b0e4f95 -r 44b84d32883c test-data/all_vcf2.fasta --- a/test-data/all_vcf2.fasta Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ ->01_1787_FL_Zoo_Jaguar_vcf ->BCG_Pasteur_Unknown_FR_SRR8886989_vcf ->02_0585_COA_TX_Fed_vcf ->BCG_Tokyo_Unknown_JP_DRR029468_vcf ->02_5877_MEX_TX_Fed_vcf ->root diff -r cd636b0e4f95 -r 44b84d32883c test-data/json_all_vcf.json --- a/test-data/json_all_vcf.json Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -{"columns":[ diff -r cd636b0e4f95 -r 44b84d32883c test-data/json_avg_mq_all_vcf.json --- a/test-data/json_avg_mq_all_vcf.json Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -{"name":null,"index":[ diff -r cd636b0e4f95 -r 44b84d32883c test-data/output_summary.html --- a/test-data/output_summary.html Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - -
Number of VCF inputs: 3
Reference: -
Total run time: - - diff -r cd636b0e4f95 -r 44b84d32883c test-data/output_summary2.html --- a/test-data/output_summary2.html Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ - - -Number of VCF inputs: 5
Reference: 89
All isolates: False

- - diff -r cd636b0e4f95 -r 44b84d32883c test-data/output_summary3.html --- a/test-data/output_summary3.html Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ - - -Number of VCF inputs: 5
Reference: 89
All isolates: False

Groupings with 5 listed:
-01_1787_FL_Zoo_Jaguar_vcfMbovis-17 -Mbovis-17G -BCG_Pasteur_Unknown_FR_SRR8886989_vcfMbovis-21 -Mbovis-21A -Mbovis-21ABCG -02_0585_COA_TX_Fed_vcfMbovis-17 -Mbovis-17A -BCG_Tokyo_Unknown_JP_DRR029468_vcfMbovis-21 -Mbovis-21A -Mbovis-21ABCG -02_5877_MEX_TX_Fed_vcfMbovis-17 -Mbovis-17A -
- - diff -r cd636b0e4f95 -r 44b84d32883c test-data/output_summary4.html --- a/test-data/output_summary4.html Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ - - -Number of VCF inputs: 5
Reference: 89
All isolates: True

Groupings with 5 listed:
- - - - - - - - - - - - - -
01_1787_FL_Zoo_Jaguar_vcfMbovis-17Mbovis-17GBCG_Pasteur_Unknown_FR_SRR8886989_vcfMbovis-21Mbovis-21AMbovis-21ABCG02_0585_COA_TX_Fed_vcfMbovis-17Mbovis-17ABCG_Tokyo_Unknown_JP_DRR029468_vcfMbovis-21Mbovis-21AMbovis-21ABCG02_5877_MEX_TX_Fed_vcfMbovis-17Mbovis-17A

- - diff -r cd636b0e4f95 -r 44b84d32883c vsnp_get_snps.xml --- a/vsnp_get_snps.xml Tue Sep 21 00:21:36 2021 +0000 +++ b/vsnp_get_snps.xml Mon Nov 15 23:14:34 2021 +0000 @@ -131,7 +131,7 @@ - + @@ -166,15 +166,31 @@ - + + + + + - + + + + + - + + + + + - + + + + + @@ -196,15 +212,31 @@ - + + + + + - + + + + + - + + + + + - + + + + + @@ -227,15 +259,31 @@ - + + + + + - + + + + + - + + + + + - + + + + + @@ -258,18 +306,46 @@ - - + + + + + + + + + + - - + + + + + + + + + + - - + + + + + + + + + + - + + + + +