| Previous changeset 47:1667e4c08344 (2019-05-07) Next changeset 49:ebfa7fd256aa (2019-05-08) |
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Commit message:
planemo upload commit 2107f35724b3f897c9414be40a9d14663cba9f4d-dirty |
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modified:
2_call_sites.xml 3_filter_regions.xml 4_merge_sites.xml 5_call_consensus.xml 6_merge_vcfs.xml 7_smp_matrix.xml |
| 2_call_sites.xml |
| diff -r 1667e4c08344 -r fc7a28de6aa0 2_call_sites.xml |
| 2_call_sites.xml |
| --- a/2_call_sites.xml Tue May 07 16:12:09 2019 -0400 +++ b/2_call_sites.xml Wed May 08 11:10:14 2019 -0400 @@ -11,7 +11,6 @@ </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 1667e4c08344 -r fc7a28de6aa0 3_filter_regions.xml |
| 3_filter_regions.xml |
| --- a/3_filter_regions.xml Tue May 07 16:12:09 2019 -0400 +++ b/3_filter_regions.xml Wed May 08 11:10:14 2019 -0400 @@ -9,7 +9,6 @@ </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 1667e4c08344 -r fc7a28de6aa0 4_merge_sites.xml |
| 4_merge_sites.xml |
| --- a/4_merge_sites.xml Tue May 07 16:12:09 2019 -0400 +++ b/4_merge_sites.xml Wed May 08 11:10:14 2019 -0400 @@ -9,7 +9,6 @@ </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 1667e4c08344 -r fc7a28de6aa0 5_call_consensus.xml |
| 5_call_consensus.xml |
| --- a/5_call_consensus.xml Tue May 07 16:12:09 2019 -0400 +++ b/5_call_consensus.xml Wed May 08 11:10:14 2019 -0400 @@ -8,7 +8,6 @@ </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)" |
| 6_merge_vcfs.xml |
| diff -r 1667e4c08344 -r fc7a28de6aa0 6_merge_vcfs.xml |
| 6_merge_vcfs.xml |
| --- a/6_merge_vcfs.xml Tue May 07 16:12:09 2019 -0400 +++ b/6_merge_vcfs.xml Wed May 08 11:10:14 2019 -0400 @@ -10,7 +10,6 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && - # env && ls -lah \$CONDA_DEFAULT_ENV/bin && ls -lah \$CONDA_DEFAULT_ENV/lib && python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf" |
| 7_smp_matrix.xml |
| diff -r 1667e4c08344 -r fc7a28de6aa0 7_smp_matrix.xml |
| 7_smp_matrix.xml |
| --- a/7_smp_matrix.xml Tue May 07 16:12:09 2019 -0400 +++ b/7_smp_matrix.xml Wed May 08 11:10:14 2019 -0400 @@ -9,7 +9,6 @@ </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 |