Mercurial > repos > jpayne > snp_pipeline

changeset 9:41bd2a5793ee

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planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Tue, 30 Jan 2018 15:55:32 -0500
parents 360e1c2bf24d
children 25b858c2f21d
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, 13 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- 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)"
--- 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                    &&
--- 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/                      &&
--- 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
--- 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/
--- 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
--- 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