| Previous changeset 8:360e1c2bf24d (2018-01-30) Next changeset 10:25b858c2f21d (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 360e1c2bf24d -r 41bd2a5793ee 1_map_reads.xml |
| 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)" |
| 2_call_sites.xml |
| diff -r 360e1c2bf24d -r 41bd2a5793ee 2_call_sites.xml |
| 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 && |
| 3_filter_regions.xml |
| diff -r 360e1c2bf24d -r 41bd2a5793ee 3_filter_regions.xml |
| 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/ && |
| 4_merge_sites.xml |
| diff -r 360e1c2bf24d -r 41bd2a5793ee 4_merge_sites.xml |
| 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 |
| 5_call_consensus.xml |
| diff -r 360e1c2bf24d -r 41bd2a5793ee 5_call_consensus.xml |
| 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/ |
| 6_merge_vcfs.xml |
| diff -r 360e1c2bf24d -r 41bd2a5793ee 6_merge_vcfs.xml |
| 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 |
| 7_smp_matrix.xml |
| diff -r 360e1c2bf24d -r 41bd2a5793ee 7_smp_matrix.xml |
| 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 |