changeset 16:44b07199be73 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Tue Aug 03 19:39:55 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

--- a/macros.xml	Mon Aug 02 21:26:57 2021 +0000
+++ b/macros.xml	Tue Aug 03 19:39:55 2021 +0000
@@ -15,7 +15,10 @@
         <requirement type="package" version="1.3.0">pandas</requirement>
     </xml>
     <xml name="pysam_requirement">
-        <requirement type="package" version="0.16.0.1">pysam</requirement>
+        <requirement type="package" version="0.15.4">pysam</requirement>
+    </xml>
+    <xml name="pyvcf_requirement">
+        <requirement type="package" version="0.6.8">pyvcf</requirement>
     </xml>
     <xml name="pyyaml_requirement">
         <requirement type="package" version="5.4.1">pyyaml</requirement>

--- a/vsnp_statistics.xml	Mon Aug 02 21:26:57 2021 +0000
+++ b/vsnp_statistics.xml	Tue Aug 03 19:39:55 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="vsnp_statistics" name="vSNP: statistics" version="@WRAPPER_VERSION@.1+galaxy0" profile="@PROFILE@">
+<tool id="vsnp_statistics" name="vSNP: statistics" version="@WRAPPER_VERSION@.2+galaxy0" profile="@PROFILE@">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -21,21 +21,19 @@
         #set read2 = $input_type_cond.read2
         #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
         ln -s '${read2}' '${read2_identifier}' &&
-    #else:
-        #set read2 = None 
     #end if
 #else:
-    #set read1 = $input_type_cond.reads_collection['forward']
+    #set read1 = $input_type_cond.reads_collection.forward
     #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
     ln -s '${read1}' '${read1_identifier}' &&
-    #set read2 = $input_type_cond.reads_collection['reverse']
+    #set read2 = $input_type_cond.reads_collection.reverse
     #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
     ln -s '${read2}' '${read2_identifier}' &&
 #end if
 
 python '$__tool_directory__/vsnp_statistics.py'
 --read1 '${read1_identifier}'
-#if $read2 is not None
+#if $input_type_cond.input_type in ["pair", "paired"]:
   --read2 '${read2_identifier}'
 #end if
 #if $read1.is_of_type('fastqsanger.gz'):