# HG changeset patch
# User jpayne
# Date 1517350463 18000
# Node ID 25b858c2f21d83253577142fb945407f412cc389
# Parent  41bd2a5793eeb6a211908610e7b19ead000cddbe
planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty

diff -r 41bd2a5793ee -r 25b858c2f21d 1_map_reads.xml
--- a/1_map_reads.xml	Tue Jan 30 15:55:32 2018 -0500
+++ b/1_map_reads.xml	Tue Jan 30 17:14:23 2018 -0500
@@ -3,7 +3,7 @@
     <requirements>
         <requirement type="package" version="2.3.4">bowtie2</requirement>
         <requirement type="package" version="1.5.11">boto3</requirement>
-        <requirement type="package" version="3.4">python</requirement>
+        <requirement type="package" version="3.4">python3</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #if $reads.reads_select == 'collection'
diff -r 41bd2a5793ee -r 25b858c2f21d 2_call_sites.xml
--- a/2_call_sites.xml	Tue Jan 30 15:55:32 2018 -0500
+++ b/2_call_sites.xml	Tue Jan 30 17:14:23 2018 -0500
@@ -7,7 +7,7 @@
         <requirement type="package">picard</requirement>
         <requirement type="package">varscan</requirement>
         <requirement type="package" version="1.5.11">boto3</requirement>
-        <requirement type="package" version="3.4">python</requirement>
+        <requirement type="package" version="3.4">python3</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
     python $__tool_directory__/snp-cache.py snp_sitecalls 
diff -r 41bd2a5793ee -r 25b858c2f21d 3_filter_regions.xml
--- a/3_filter_regions.xml	Tue Jan 30 15:55:32 2018 -0500
+++ b/3_filter_regions.xml	Tue Jan 30 17:14:23 2018 -0500
@@ -5,7 +5,7 @@
         <requirement type="package" version="1.0.6">bzip2</requirement>
         <requirement type="package" version="1.0.1">snp-pipeline</requirement>
         <requirement type="package" version="1.5.11">boto3</requirement>
-        <requirement type="package" version="3.4">python</requirement>
+        <requirement type="package" version="3.4">python3</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         mkdir -p ./samples/sample/                      &&
diff -r 41bd2a5793ee -r 25b858c2f21d 4_merge_sites.xml
--- a/4_merge_sites.xml	Tue Jan 30 15:55:32 2018 -0500
+++ b/4_merge_sites.xml	Tue Jan 30 17:14:23 2018 -0500
@@ -4,7 +4,7 @@
         <requirement type="package" version="2.2.6">bowtie2</requirement>
         <requirement type="package" version="1.2">samtools</requirement>
         <requirement type="package">snp-pipeline</requirement>
-        <requirement type="package" version="3.4">python</requirement>
+        <requirement type="package" version="3.4">python3</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         python $__tool_directory__/snp-wind.py ./
diff -r 41bd2a5793ee -r 25b858c2f21d 5_call_consensus.xml
--- a/5_call_consensus.xml	Tue Jan 30 15:55:32 2018 -0500
+++ b/5_call_consensus.xml	Tue Jan 30 17:14:23 2018 -0500
@@ -3,7 +3,7 @@
     <requirements>
         <requirement type="package" version="1.0.1">snp-pipeline</requirement>
         <requirement type="package" version="1.5.11">boto3</requirement>
-        <requirement type="package" version="3.4">python</requirement>
+        <requirement type="package" version="3.4">python3</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #set $identifier = $call_pileup.name.split(' ')[0]
diff -r 41bd2a5793ee -r 25b858c2f21d 6_merge_vcfs.xml
--- a/6_merge_vcfs.xml	Tue Jan 30 15:55:32 2018 -0500
+++ b/6_merge_vcfs.xml	Tue Jan 30 17:14:23 2018 -0500
@@ -1,10 +1,10 @@
 <tool id="merge_vcfs" name="6. Merge VCFs" version="1.0.1" profile="16.10">
     <description>into a multi-sample VCF with consensus SNPs</description>
     <requirements>
-        <requirement type="package" version="1.3.1">bcftools</requirement>
+        <requirement type="package" version="1.6">bcftools</requirement>
         <requirement type="package" version="1.0.1">snp-pipeline</requirement>
         <requirement type="package">tabix</requirement>
-        <requirement type="package" version="3.4">python</requirement>
+        <requirement type="package" version="3.4">python3</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
diff -r 41bd2a5793ee -r 25b858c2f21d 7_smp_matrix.xml
--- a/7_smp_matrix.xml	Tue Jan 30 15:55:32 2018 -0500
+++ b/7_smp_matrix.xml	Tue Jan 30 17:14:23 2018 -0500
@@ -3,7 +3,7 @@
     <requirements>
         <requirement type="package" version="1.0.1">snp-pipeline</requirement>
         <requirement type="package">tabix</requirement>
-        <requirement type="package" version="3.4">python</requirement>
+        <requirement type="package" version="3.4">python3</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         python $__tool_directory__/snp-wind.py ./ -p "consensus.fasta"