# 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
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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 @@
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Combine multiple Snippy outputs into a core SNP alignment
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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 @@
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Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
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- macros.xml
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+ macros.xml
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+ ]]>
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outputs and 'outcon' in outputs
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outputs and 'outbam' in outputs
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For a much more in depth description of snippy and how it works, see https://github.com/tseemann/snippy
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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 @@
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+ value, dbkey, name, path
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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 @@
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+ value, dbkey, name, path
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