Mercurial > repos > jpayne > snp_pipeline

changeset 10:25b858c2f21d

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planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Tue, 30 Jan 2018 17:14:23 -0500
parents 41bd2a5793ee
children 772f310d2506
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, 8 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- 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'
--- 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 
--- 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/                      &&
--- 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 ./
--- 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]
--- 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"
--- 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"