| Previous changeset 5:5191246bc2e2 (2018-01-25) Next changeset 7:13539c458a6e (2018-01-29) |
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Commit message:
planemo upload commit b'7f6183b769772449fbcee903686b8d5ec5b7439f\n'-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 5191246bc2e2 -r 62191abf5426 1_map_reads.xml |
| 1_map_reads.xml |
| --- a/1_map_reads.xml Thu Jan 25 13:55:20 2018 -0500 +++ b/1_map_reads.xml Mon Jan 29 13:56:19 2018 -0500 @@ -3,6 +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> </requirements> <command detect_errors="exit_code"><![CDATA[ #if $reads.reads_select == 'collection' |
| 2_call_sites.xml |
| diff -r 5191246bc2e2 -r 62191abf5426 2_call_sites.xml |
| 2_call_sites.xml |
| --- a/2_call_sites.xml Thu Jan 25 13:55:20 2018 -0500 +++ b/2_call_sites.xml Mon Jan 29 13:56:19 2018 -0500 @@ -7,6 +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> </requirements> <command detect_errors="exit_code"><![CDATA[ $__tool_directory__/snp-cache.py snp_sitecalls |
| 3_filter_regions.xml |
| diff -r 5191246bc2e2 -r 62191abf5426 3_filter_regions.xml |
| 3_filter_regions.xml |
| --- a/3_filter_regions.xml Thu Jan 25 13:55:20 2018 -0500 +++ b/3_filter_regions.xml Mon Jan 29 13:56:19 2018 -0500 @@ -5,6 +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> </requirements> <command detect_errors="exit_code"><![CDATA[ mkdir -p ./samples/sample/ && |
| 4_merge_sites.xml |
| diff -r 5191246bc2e2 -r 62191abf5426 4_merge_sites.xml |
| 4_merge_sites.xml |
| --- a/4_merge_sites.xml Thu Jan 25 13:55:20 2018 -0500 +++ b/4_merge_sites.xml Mon Jan 29 13:56:19 2018 -0500 @@ -4,6 +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> </requirements> <command detect_errors="exit_code"><![CDATA[ $__tool_directory__/snp-wind.py ./ |
| 5_call_consensus.xml |
| diff -r 5191246bc2e2 -r 62191abf5426 5_call_consensus.xml |
| 5_call_consensus.xml |
| --- a/5_call_consensus.xml Thu Jan 25 13:55:20 2018 -0500 +++ b/5_call_consensus.xml Mon Jan 29 13:56:19 2018 -0500 @@ -3,6 +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> </requirements> <command detect_errors="exit_code"><![CDATA[ #set $identifier = $call_pileup.name.split(' ')[0] |
| 6_merge_vcfs.xml |
| diff -r 5191246bc2e2 -r 62191abf5426 6_merge_vcfs.xml |
| 6_merge_vcfs.xml |
| --- a/6_merge_vcfs.xml Thu Jan 25 13:55:20 2018 -0500 +++ b/6_merge_vcfs.xml Mon Jan 29 13:56:19 2018 -0500 @@ -4,6 +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> </requirements> <command detect_errors="exit_code"><![CDATA[ $__tool_directory__/snp-wind.py ./ -p "consensus.vcf" |
| 7_smp_matrix.xml |
| diff -r 5191246bc2e2 -r 62191abf5426 7_smp_matrix.xml |
| 7_smp_matrix.xml |
| --- a/7_smp_matrix.xml Thu Jan 25 13:55:20 2018 -0500 +++ b/7_smp_matrix.xml Mon Jan 29 13:56:19 2018 -0500 @@ -3,6 +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> </requirements> <command detect_errors="exit_code"><![CDATA[ $__tool_directory__/snp-wind.py ./ -p "consensus.fasta" |