# HG changeset patch # User iuc # Date 1568367921 14400 # Node ID 0aa87d97847f1425971f52e49762c8286b28c5a1 # Parent 9bccc8404a3c92fac8eb2886d39a84217ab9f3c8 "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" diff -r 9bccc8404a3c -r 0aa87d97847f macros.xml --- a/macros.xml Thu Jul 11 09:41:13 2019 -0400 +++ b/macros.xml Fri Sep 13 05:45:21 2019 -0400 @@ -10,7 +10,53 @@ - 4.3.6 + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4.4.3 diff -r 9bccc8404a3c -r 0aa87d97847f snippy-core.xml --- a/snippy-core.xml Thu Jul 11 09:41:13 2019 -0400 +++ b/snippy-core.xml Fri Sep 13 05:45:21 2019 -0400 @@ -1,5 +1,5 @@ - + Combine multiple Snippy outputs into a core SNP alignment @@ -8,19 +8,20 @@ - + @@ -48,7 +49,19 @@ - + + + + + + + + + + + + + diff -r 9bccc8404a3c -r 0aa87d97847f snippy.xml --- a/snippy.xml Thu Jul 11 09:41:13 2019 -0400 +++ b/snippy.xml Fri Sep 13 05:45:21 2019 -0400 @@ -1,31 +1,22 @@ - + Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. - - - macros.xml - - - + + + macros.xml + + + + ]]> - - - + @@ -115,7 +104,6 @@ - @@ -145,9 +133,6 @@ outputs and 'outcon' in outputs - - outputs and 'outdep' in outputs - outputs and 'outbam' in outputs @@ -159,8 +144,12 @@ - - + + + + + + @@ -171,8 +160,11 @@ - - + + + + + @@ -183,8 +175,11 @@ - - + + + + + @@ -199,8 +194,25 @@ - - + + + + + + + + + + + + + + + + + + + @@ -247,7 +259,7 @@ For a much more in depth description of snippy and how it works, see https://github.com/tseemann/snippy - ]]> - + ]]> + diff -r 9bccc8404a3c -r 0aa87d97847f test-data/a_fna_ref_mincov_2_minqual_60.snps.txt --- a/test-data/a_fna_ref_mincov_2_minqual_60.snps.txt Thu Jul 11 09:41:13 2019 -0400 +++ b/test-data/a_fna_ref_mincov_2_minqual_60.snps.txt Fri Sep 13 05:45:21 2019 -0400 @@ -2,5 +2,5 @@ ReadFiles a_1.fastq a_2.fastq Reference reference.fasta ReferenceSize 700 -Software snippy 4.3.6 +Software snippy 4.4.3 VariantTotal 0 diff -r 9bccc8404a3c -r 0aa87d97847f test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Fri Sep 13 05:45:21 2019 -0400 @@ -0,0 +1,20 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +# +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# +test_id test_dbkey test display name ${__HERE__}/ref.fna + diff -r 9bccc8404a3c -r 0aa87d97847f test-data/b_2_fna_ref_mincov_2_minqual_60.snps.gff --- a/test-data/b_2_fna_ref_mincov_2_minqual_60.snps.gff Thu Jul 11 09:41:13 2019 -0400 +++ b/test-data/b_2_fna_ref_mincov_2_minqual_60.snps.gff Fri Sep 13 05:45:21 2019 -0400 @@ -1,2 +1,2 @@ ##gff-version 3 -reference snippy:4.3.6 variation 4 4 . . 0 note=snp A=>T T:5 A:0 +reference snippy:4.4.3 variation 4 4 . . 0 note=snp A=>T T:5 A:0 diff -r 9bccc8404a3c -r 0aa87d97847f test-data/b_fna_ref_mincov_2_minqual_60.snps.gff --- a/test-data/b_fna_ref_mincov_2_minqual_60.snps.gff Thu Jul 11 09:41:13 2019 -0400 +++ b/test-data/b_fna_ref_mincov_2_minqual_60.snps.gff Fri Sep 13 05:45:21 2019 -0400 @@ -1,2 +1,2 @@ ##gff-version 3 -reference snippy:4.3.6 variation 4 4 . . 0 note=snp A=>T T:10 A:0 +reference snippy:4.4.3 variation 4 4 . . 0 note=snp A=>T T:10 A:0 diff -r 9bccc8404a3c -r 0aa87d97847f test-data/b_fna_ref_mincov_2_minqual_60.snps.txt --- a/test-data/b_fna_ref_mincov_2_minqual_60.snps.txt Thu Jul 11 09:41:13 2019 -0400 +++ b/test-data/b_fna_ref_mincov_2_minqual_60.snps.txt Fri Sep 13 05:45:21 2019 -0400 @@ -2,6 +2,6 @@ ReadFiles b_1.fastq b_2.fastq Reference reference.fasta ReferenceSize 700 -Software snippy 4.3.6 +Software snippy 4.4.3 Variant-SNP 1 VariantTotal 1 diff -r 9bccc8404a3c -r 0aa87d97847f tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Fri Sep 13 05:45:21 2019 -0400 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +# +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# \ No newline at end of file diff -r 9bccc8404a3c -r 0aa87d97847f tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Sep 13 05:45:21 2019 -0400 @@ -0,0 +1,8 @@ + + + + + value, dbkey, name, path + +
+
diff -r 9bccc8404a3c -r 0aa87d97847f tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Sep 13 05:45:21 2019 -0400 @@ -0,0 +1,8 @@ + + + + + value, dbkey, name, path + +
+