# HG changeset patch
# User greg
# Date 1627938799 0
# Node ID ce1f889b3340144ad7ca7cb648b12bfdc8bf9d80
# Parent  3c4dba2b5b141608f658a8739fccc4ddfaef3820
Uploaded

diff -r 3c4dba2b5b14 -r ce1f889b3340 .shed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Mon Aug 02 21:13:19 2021 +0000
@@ -0,0 +1,13 @@
+name: vsnp_statistics
+owner: greg
+description: |
+  Contains a tool that produces an Excel spreadsheet containing statistics for samples and associated metrics files.
+homepage_url: https://github.com/USDA-VS/vSNP
+long_description: |
+  Contains a tool Accepts a single fastqsanger sample, a set of paired read samples, or a collections of samples
+  along with associated SAMtools idxstats and vSNP zero coverage metrics files and extracts information from them
+  to produce an Excel spreadsheet containing statistics for each sample.
+remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_statistics
+type: unrestricted
+categories:
+  - Sequence Analysis
diff -r 3c4dba2b5b14 -r ce1f889b3340 test-data/vsnp_statistics4.tabular
--- a/test-data/vsnp_statistics4.tabular	Mon Aug 02 16:46:34 2021 +0000
+++ b/test-data/vsnp_statistics4.tabular	Mon Aug 02 21:13:19 2021 +0000
@@ -1,2 +1,2 @@
 Reference	Read1 FASTQ	File Size	Reads	Mean Read Length	Mean Read Quality	Reads Passing Q30	Read2 FASTQ	File Size	Reads	Mean Read Length	Mean Read Quality	Reads Passing Q30	Total Reads	All Mapped Reads	Unmapped Reads	Unmapped Reads Percentage of Total	Reference with Coverage	Average Depth of Coverage	Good SNP Count
-89	13-1941-6_S4_L001_R1_600000_fastq_gz	8.7 KB	25	100.0	65.7	      1.00	13-1941-6_S4_L001_R2_600000_fastq_gz	8.5 KB	25	100.0	66.3	      1.00	50	46	4	      0.08	0.16%	0.002146	0
+89	forward	8.7 KB	25	100.0	65.7	      1.00	reverse	8.5 KB	25	100.0	66.3	      1.00	50	46	4	      0.08	0.16%	0.002146	0
diff -r 3c4dba2b5b14 -r ce1f889b3340 vsnp_statistics.xml
--- a/vsnp_statistics.xml	Mon Aug 02 16:46:34 2021 +0000
+++ b/vsnp_statistics.xml	Mon Aug 02 21:13:19 2021 +0000
@@ -26,10 +26,10 @@
     #end if
 #else:
     #set read1 = $input_type_cond.reads_collection['forward']
-    #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name))
+    #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
     ln -s '${read1}' '${read1_identifier}' &&
     #set read2 = $input_type_cond.reads_collection['reverse']
-    #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.name))
+    #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
     ln -s '${read2}' '${read2_identifier}' &&
 #end if