# HG changeset patch
# User greg
# Date 1623862444 0
# Node ID 77eb4c46ee881f3ba122215874070d5fe5c88727
# Parent  36bdf8b439ed5cc375854821b8c57e08ca1509e8
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_determine_ref_from_data commit fab4644851280deb554f15f4b5f4770f8700e2c2"

diff -r 36bdf8b439ed -r 77eb4c46ee88 .shed.yml
--- a/.shed.yml	Sun Jan 03 16:13:22 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-name: vsnp_determine_ref_from_data
-owner: greg
-description: |
-  Contains a tool that sniffs bacterial genome samples to discover the primary species within the sample.
-homepage_url: https://github.com/USDA-VS/vSNP
-long_description: |
-  Contains a tool that sniffs bacterial genome samples to discover the primary species within the sample.
-remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_determine_ref_from_data
-type: unrestricted
-categories:
-  - Sequence Analysis
diff -r 36bdf8b439ed -r 77eb4c46ee88 test-data/CMC_20E1_R1.fastq.gz
Binary file test-data/CMC_20E1_R1.fastq.gz has changed
diff -r 36bdf8b439ed -r 77eb4c46ee88 test-data/CMC_20E1_R2.fastq.gz
Binary file test-data/CMC_20E1_R2.fastq.gz has changed
diff -r 36bdf8b439ed -r 77eb4c46ee88 test-data/Mcap_Deer_DE_SRR650221.fastq.gz
Binary file test-data/Mcap_Deer_DE_SRR650221.fastq.gz has changed
diff -r 36bdf8b439ed -r 77eb4c46ee88 test-data/NC_002945v4.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_002945v4.yml	Wed Jun 16 16:54:04 2021 +0000
@@ -0,0 +1,5 @@
+bovis:
+ - '11001110'
+ - '11011110'
+ - '11001100'
+
diff -r 36bdf8b439ed -r 77eb4c46ee88 test-data/output_dbkey.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_dbkey.txt	Wed Jun 16 16:54:04 2021 +0000
@@ -0,0 +1,1 @@
+AF2122
\ No newline at end of file
diff -r 36bdf8b439ed -r 77eb4c46ee88 test-data/output_metrics.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_metrics.txt	Wed Jun 16 16:54:04 2021 +0000
@@ -0,0 +1,6 @@
+Sample: Mcap_Deer_DE_SRR650221_fastq_gz
+Brucella counts: 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+TB counts: 2,2,0,0,4,5,0,0,
+Para counts: 0,0,0,
+Group: TB
+dbkey: AF2122
diff -r 36bdf8b439ed -r 77eb4c46ee88 test-data/paired_collection_metrics.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_collection_metrics.txt	Wed Jun 16 16:54:04 2021 +0000
@@ -0,0 +1,6 @@
+Sample: CMC_20E1_R1_fastq_gz
+Brucella counts: 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+TB counts: 4,4,0,0,8,10,0,0,
+Para counts: 0,0,0,
+Group: TB
+dbkey: AF2122
diff -r 36bdf8b439ed -r 77eb4c46ee88 test-data/paired_dbkey.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_dbkey.txt	Wed Jun 16 16:54:04 2021 +0000
@@ -0,0 +1,1 @@
+AF2122
\ No newline at end of file
diff -r 36bdf8b439ed -r 77eb4c46ee88 test-data/paired_metrics.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_metrics.txt	Wed Jun 16 16:54:04 2021 +0000
@@ -0,0 +1,6 @@
+Sample: CMC_20E1_R1_fastq_gz
+Brucella counts: 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+TB counts: 4,4,0,0,8,10,0,0,
+Para counts: 0,0,0,
+Group: TB
+dbkey: AF2122
diff -r 36bdf8b439ed -r 77eb4c46ee88 test-data/vsnp_dnaprints.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vsnp_dnaprints.loc	Wed Jun 16 16:54:04 2021 +0000
@@ -0,0 +1,5 @@
+## vSNP DNAprints files
+#Value	Name	Path	Description
+AF2122	Mycobacterium_AF2122/NC_002945v4.yml	${__HERE__}/NC_002945v4.yml	DNAprints file for Mycobacterium bovis AF2122/97
+#NC_006932	Brucella_abortus1/NC_006932-NC_006933.yml	/vsnp/NC_006932/Brucella_abortus1/NC_006932-NC_006933.yml	DNAprints file for Brucella abortus bv. 1 str. 9-941
+
diff -r 36bdf8b439ed -r 77eb4c46ee88 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Jun 16 16:54:04 2021 +0000
@@ -0,0 +1,8 @@
+<tables>
+    <!-- Location of dnaprints files for vsnp_dtermine_ref_from_data tool -->
+    <table name="vsnp_dnaprints" comment_char="#">
+        <columns>value, name, path, description</columns>
+        <file path="tool-data/vsnp_dnaprints.loc" />
+    </table>
+</tables>
+
diff -r 36bdf8b439ed -r 77eb4c46ee88 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Wed Jun 16 16:54:04 2021 +0000
@@ -0,0 +1,7 @@
+<tables>
+    <table name="vsnp_dnaprints" comment_char="#">
+        <columns>value, name, path, description</columns>
+        <file path="${__HERE__}/test-data/vsnp_dnaprints.loc" />
+    </table>
+</tables>
+