Mercurial > repos > drosofff > lumpy
changeset 7:e833b178b94b draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 834a0ca8b5cc29307a03c1b22a372152ed064abd
| author | drosofff |
|---|---|
| date | Fri, 09 Dec 2016 06:13:27 -0500 |
| parents | e9db5497e675 |
| children | 382ffb8e0caa |
| files | lumpy.xml |
| diffstat | 1 files changed, 22 insertions(+), 3 deletions(-) [+] |
line wrap: on
line diff
--- a/lumpy.xml Wed Dec 07 12:35:43 2016 -0500 +++ b/lumpy.xml Fri Dec 09 06:13:27 2016 -0500 @@ -29,7 +29,10 @@ |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt && mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) && stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) && - lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt + lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt + #if $output_format == "BEDPE": + -b + #end if -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$analysis_type.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold -sr id:input.bam,bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf && mv input.discordants.bam $discordants && @@ -41,6 +44,9 @@ #if $seq_method.seq_method_list == "single-read": samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" && lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt + #if $output_format == "BEDPE": + -b + #end if -sr id:input.bam,bam_file:input.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf && mv input.splitters.unsorted.bam $splits && mv output.vcf $vcf_call @@ -68,6 +74,9 @@ stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) && stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) && lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt + #if $output_format == "BEDPE": + -b + #end if -pe id:inputA.bam,bam_file:input.A.discordants.bam,histo_file:input.A.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$analysis_type.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold -pe id:inputB.bam,bam_file:input.B.discordants.bam,histo_file:input.B.lib.histo,mean:"\$meanB",stdev:"\$stdevA",read_length:$analysis_type.readLengthB,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold -sr id:inputA.bam,bam_file:input.A.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold @@ -85,6 +94,9 @@ samtools view -h input.A.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.A.splitters.unsorted.bam" && samtools view -h input.B.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.B.splitters.unsorted.bam" && lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt + #if $output_format == "BEDPE": + -b + #end if -sr id:input.A.bam,bam_file:input.A.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold -sr id:input.B.bam,bam_file:input.B.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf && mv input.A.splitters.unsorted.bam $splits && @@ -142,7 +154,10 @@ </when> </conditional> - + <param help="get variant calling in vcf or BEDPE format" label="variant calling format" name="output_format" type="select"> + <option selected="True" value="vcf">vcf</option> + <option value="BEDPE">BEDPE</option> + </param> </inputs> <outputs> @@ -164,7 +179,11 @@ <filter>seq_method['seq_method_list'] == "paired-end"</filter> <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> </data> - <data format="vcf" name="vcf_call" label="Lumpy Variant Calling (vcf format)"/> + <data format="vcf" name="vcf_call" label="Lumpy Variant Calling"> + <change_format> + <when format="tabular" input="output_format" value="BEDPE" /> + </change_format> + </data> </outputs> <tests>