# HG changeset patch
# User jpayne
# Date 1517345732 18000
# Node ID 41bd2a5793eeb6a211908610e7b19ead000cddbe
# Parent  360e1c2bf24d438796035cfc1769973b2cdab129
planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty

diff -r 360e1c2bf24d -r 41bd2a5793ee 1_map_reads.xml
--- a/1_map_reads.xml	Tue Jan 30 12:33:48 2018 -0500
+++ b/1_map_reads.xml	Tue Jan 30 15:55:32 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="3.5">python</requirement>
+        <requirement type="package" version="3.4">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #if $reads.reads_select == 'collection'
@@ -13,7 +13,7 @@
             export files="$forward $reverse"                    &&
             export params="-1 $forward -2 $reverse"             &&
         #end if
-        ${__tool_directory__}/snp-cache.py snp_mapped_reads 
+        python ${__tool_directory__}/snp-cache.py snp_mapped_reads 
             "\$(md5sum  $reference
                         \$files 
                         | cut -c -32 | md5sum | cut -c -32)"
diff -r 360e1c2bf24d -r 41bd2a5793ee 2_call_sites.xml
--- a/2_call_sites.xml	Tue Jan 30 12:33:48 2018 -0500
+++ b/2_call_sites.xml	Tue Jan 30 15:55:32 2018 -0500
@@ -7,10 +7,10 @@
         <requirement type="package">picard</requirement>
         <requirement type="package">varscan</requirement>
         <requirement type="package" version="1.5.11">boto3</requirement>
-        <requirement type="package" version="3.5">python</requirement>
+        <requirement type="package" version="3.4">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-    $__tool_directory__/snp-cache.py snp_sitecalls 
+    python $__tool_directory__/snp-cache.py snp_sitecalls 
         "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)"
         -c "
             cp $input ./reference.fasta                    &&
diff -r 360e1c2bf24d -r 41bd2a5793ee 3_filter_regions.xml
--- a/3_filter_regions.xml	Tue Jan 30 12:33:48 2018 -0500
+++ b/3_filter_regions.xml	Tue Jan 30 15:55:32 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="3.5">python</requirement>
+        <requirement type="package" version="3.4">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         mkdir -p ./samples/sample/                      &&
diff -r 360e1c2bf24d -r 41bd2a5793ee 4_merge_sites.xml
--- a/4_merge_sites.xml	Tue Jan 30 12:33:48 2018 -0500
+++ b/4_merge_sites.xml	Tue Jan 30 15:55:32 2018 -0500
@@ -4,10 +4,10 @@
         <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="3.5">python</requirement>
+        <requirement type="package" version="3.4">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        $__tool_directory__/snp-wind.py ./
+        python $__tool_directory__/snp-wind.py ./
                 #for $call in $calls
                     -n $call.element_identifier -f $call
                 #end for
diff -r 360e1c2bf24d -r 41bd2a5793ee 5_call_consensus.xml
--- a/5_call_consensus.xml	Tue Jan 30 12:33:48 2018 -0500
+++ b/5_call_consensus.xml	Tue Jan 30 15:55:32 2018 -0500
@@ -3,11 +3,11 @@
     <requirements>
         <requirement type="package" version="1.0.1">snp-pipeline</requirement>
         <requirement type="package" version="1.5.11">boto3</requirement>
-        <requirement type="package" version="3.5">python</requirement>
+        <requirement type="package" version="3.4">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #set $identifier = $call_pileup.name.split(' ')[0]
-        $__tool_directory__/snp-cache.py snp_consenus_calls
+        python $__tool_directory__/snp-cache.py snp_consenus_calls
             "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)"
             -c "
                 mkdir ./$identifier/
diff -r 360e1c2bf24d -r 41bd2a5793ee 6_merge_vcfs.xml
--- a/6_merge_vcfs.xml	Tue Jan 30 12:33:48 2018 -0500
+++ b/6_merge_vcfs.xml	Tue Jan 30 15:55:32 2018 -0500
@@ -4,10 +4,10 @@
         <requirement type="package" version="1.3.1">bcftools</requirement>
         <requirement type="package" version="1.0.1">snp-pipeline</requirement>
         <requirement type="package">tabix</requirement>
-        <requirement type="package" version="3.5">python</requirement>
+        <requirement type="package" version="3.4">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
+        python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
             #for $vcf in $vcfs
                 -n $vcf.element_identifier -f $vcf
             #end for
diff -r 360e1c2bf24d -r 41bd2a5793ee 7_smp_matrix.xml
--- a/7_smp_matrix.xml	Tue Jan 30 12:33:48 2018 -0500
+++ b/7_smp_matrix.xml	Tue Jan 30 15:55:32 2018 -0500
@@ -3,10 +3,10 @@
     <requirements>
         <requirement type="package" version="1.0.1">snp-pipeline</requirement>
         <requirement type="package">tabix</requirement>
-        <requirement type="package" version="3.5">python</requirement>
+        <requirement type="package" version="3.4">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        $__tool_directory__/snp-wind.py ./ -p "consensus.fasta"
+        python $__tool_directory__/snp-wind.py ./ -p "consensus.fasta"
             #for $fa in sorted($cons, key=lambda f: f.element_identifier)
                 -n $fa.element_identifier -f $fa
             #end for