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changeset 7:13539c458a6e

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planemo upload commit b'7f6183b769772449fbcee903686b8d5ec5b7439f\n'-dirty
author jpayne
date Mon, 29 Jan 2018 16:19:16 -0500
parents 62191abf5426
children 360e1c2bf24d
files 1_map_reads.xml 2_call_sites.xml 3_filter_regions.xml 4_merge_sites.xml 5_call_consensus.xml 6_merge_vcfs.xml 7_smp_matrix.xml
diffstat 7 files changed, 7 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/1_map_reads.xml	Mon Jan 29 13:56:19 2018 -0500
+++ b/1_map_reads.xml	Mon Jan 29 16:19:16 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">package_python_3_5</requirement>
+        <requirement type="package" version="3.6">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #if $reads.reads_select == 'collection'
--- a/2_call_sites.xml	Mon Jan 29 13:56:19 2018 -0500
+++ b/2_call_sites.xml	Mon Jan 29 16:19:16 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">package_python_3_5</requirement>
+        <requirement type="package" version="3.6">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
     $__tool_directory__/snp-cache.py snp_sitecalls 
--- a/3_filter_regions.xml	Mon Jan 29 13:56:19 2018 -0500
+++ b/3_filter_regions.xml	Mon Jan 29 16:19:16 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">package_python_3_5</requirement>
+        <requirement type="package" version="3.6">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         mkdir -p ./samples/sample/                      &&
--- a/4_merge_sites.xml	Mon Jan 29 13:56:19 2018 -0500
+++ b/4_merge_sites.xml	Mon Jan 29 16:19:16 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">package_python_3_5</requirement>
+        <requirement type="package" version="3.6">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         $__tool_directory__/snp-wind.py ./
--- a/5_call_consensus.xml	Mon Jan 29 13:56:19 2018 -0500
+++ b/5_call_consensus.xml	Mon Jan 29 16:19:16 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">package_python_3_5</requirement>
+        <requirement type="package" version="3.6">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #set $identifier = $call_pileup.name.split(' ')[0]
--- a/6_merge_vcfs.xml	Mon Jan 29 13:56:19 2018 -0500
+++ b/6_merge_vcfs.xml	Mon Jan 29 16:19:16 2018 -0500
@@ -4,7 +4,7 @@
         <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">package_python_3_5</requirement>
+        <requirement type="package" version="3.6">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
--- a/7_smp_matrix.xml	Mon Jan 29 13:56:19 2018 -0500
+++ b/7_smp_matrix.xml	Mon Jan 29 16:19:16 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">package_python_3_5</requirement>
+        <requirement type="package" version="3.6">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         $__tool_directory__/snp-wind.py ./ -p "consensus.fasta"