| Previous changeset 39:1fe3b14f7f1b (2018-02-14) Next changeset 41:9022b00a9198 (2018-03-01) |
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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 7_smp_matrix.xml |
| 1_map_reads.xml |
| diff -r 1fe3b14f7f1b -r 02733e77f84f 1_map_reads.xml |
| 1_map_reads.xml |
| --- a/1_map_reads.xml Wed Feb 14 13:06:44 2018 -0500 +++ b/1_map_reads.xml Wed Feb 14 13:10:23 2018 -0500 @@ -7,6 +7,7 @@ <!-- <requirement type="package" version="3.5">python</requirement> --> </requirements> <command detect_errors="exit_code"><![CDATA[ + export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && env && #if $reads.reads_select == 'collection' export files="$reads.coll.forward $reads.coll.reverse" && |
| 2_call_sites.xml |
| diff -r 1fe3b14f7f1b -r 02733e77f84f 2_call_sites.xml |
| 2_call_sites.xml |
| --- a/2_call_sites.xml Wed Feb 14 13:06:44 2018 -0500 +++ b/2_call_sites.xml Wed Feb 14 13:10:23 2018 -0500 @@ -10,6 +10,8 @@ <!-- <requirement type="package" version="3.5">python</requirement> --> </requirements> <command detect_errors="exit_code"><![CDATA[ + export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && + env && python $__tool_directory__/snp-cache.py snp_sitecalls "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)" -c " |
| 3_filter_regions.xml |
| diff -r 1fe3b14f7f1b -r 02733e77f84f 3_filter_regions.xml |
| 3_filter_regions.xml |
| --- a/3_filter_regions.xml Wed Feb 14 13:06:44 2018 -0500 +++ b/3_filter_regions.xml Wed Feb 14 13:10:23 2018 -0500 @@ -8,6 +8,8 @@ <!-- <requirement type="package" version="3.5">python</requirement> --> </requirements> <command detect_errors="exit_code"><![CDATA[ + export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && + env && mkdir -p ./samples/sample/ && cp $calls ./samples/sample/var.flt.vcf && echo "\$PWD/samples/sample" > ./alignment.txt && |
| 4_merge_sites.xml |
| diff -r 1fe3b14f7f1b -r 02733e77f84f 4_merge_sites.xml |
| 4_merge_sites.xml |
| --- a/4_merge_sites.xml Wed Feb 14 13:06:44 2018 -0500 +++ b/4_merge_sites.xml Wed Feb 14 13:10:23 2018 -0500 @@ -8,6 +8,8 @@ <!-- <requirement type="package" version="3.5">python</requirement> --> </requirements> <command detect_errors="exit_code"><![CDATA[ + export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && + env && python $__tool_directory__/snp-wind.py ./ #for $call in $calls -n $call.element_identifier -f $call |
| 5_call_consensus.xml |
| diff -r 1fe3b14f7f1b -r 02733e77f84f 5_call_consensus.xml |
| 5_call_consensus.xml |
| --- a/5_call_consensus.xml Wed Feb 14 13:06:44 2018 -0500 +++ b/5_call_consensus.xml Wed Feb 14 13:10:23 2018 -0500 @@ -7,6 +7,8 @@ <!-- <requirement type="package" version="3.5">python</requirement> --> </requirements> <command detect_errors="exit_code"><![CDATA[ + export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && + env && #set $identifier = $call_pileup.name.split(' ')[0] python $__tool_directory__/snp-cache.py snp_consenus_calls "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)" |
| 7_smp_matrix.xml |
| diff -r 1fe3b14f7f1b -r 02733e77f84f 7_smp_matrix.xml |
| 7_smp_matrix.xml |
| --- a/7_smp_matrix.xml Wed Feb 14 13:06:44 2018 -0500 +++ b/7_smp_matrix.xml Wed Feb 14 13:10:23 2018 -0500 @@ -8,6 +8,8 @@ <!-- <requirement type="package" version="3.5">python</requirement> --> </requirements> <command detect_errors="exit_code"><![CDATA[ + export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && + env && 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 |