| Previous changeset 9:41bd2a5793ee (2018-01-30) Next changeset 11:772f310d2506 (2018-01-30) |
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Commit message:
planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty |
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modified:
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 |
| 1_map_reads.xml |
| diff -r 41bd2a5793ee -r 25b858c2f21d 1_map_reads.xml |
| 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' |
| 2_call_sites.xml |
| diff -r 41bd2a5793ee -r 25b858c2f21d 2_call_sites.xml |
| 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 |
| 3_filter_regions.xml |
| diff -r 41bd2a5793ee -r 25b858c2f21d 3_filter_regions.xml |
| 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/ && |
| 4_merge_sites.xml |
| diff -r 41bd2a5793ee -r 25b858c2f21d 4_merge_sites.xml |
| 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 ./ |
| 5_call_consensus.xml |
| diff -r 41bd2a5793ee -r 25b858c2f21d 5_call_consensus.xml |
| 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] |
| 6_merge_vcfs.xml |
| diff -r 41bd2a5793ee -r 25b858c2f21d 6_merge_vcfs.xml |
| 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" |
| 7_smp_matrix.xml |
| diff -r 41bd2a5793ee -r 25b858c2f21d 7_smp_matrix.xml |
| 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" |