# HG changeset patch
# User greg
# Date 1628083637 0
# Node ID 076069733de73d4e28eab4c97d3ff315da091371
# Parent  932e517b577916e24636a100fcbdc836676cb684
Uploaded

diff -r 932e517b5779 -r 076069733de7 .shed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Wed Aug 04 13:27:17 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 932e517b5779 -r 076069733de7 test-data/vsnp_statistics4.tabular
--- a/test-data/vsnp_statistics4.tabular	Tue Aug 03 19:52:56 2021 +0000
+++ b/test-data/vsnp_statistics4.tabular	Wed Aug 04 13:27:17 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	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
+89	Unnamed Collection_R1	8.7 KB	25	100.0	65.7	      1.00	Unnamed Collection_R2	8.5 KB	25	100.0	66.3	      1.00	50	46	4	      0.08	0.16%	0.002146	0
diff -r 932e517b5779 -r 076069733de7 vsnp_statistics.xml
--- a/vsnp_statistics.xml	Tue Aug 03 19:52:56 2021 +0000
+++ b/vsnp_statistics.xml	Wed Aug 04 13:27:17 2021 +0000
@@ -23,11 +23,12 @@
         ln -s '${read2}' '${read2_identifier}' &&
     #end if
 #else:
+    #set identifier = re.sub('[^\s\w\-]', '_', str($input_type_cond.reads_collection.element_identifier))
     #set read1 = $input_type_cond.reads_collection.forward
-    #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
+    #set read1_identifier = $identifier + '_R1'
     ln -s '${read1}' '${read1_identifier}' &&
     #set read2 = $input_type_cond.reads_collection.reverse
-    #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
+    #set read2_identifier = $identifier + '_R2'
     ln -s '${read2}' '${read2_identifier}' &&
 #end if