Previous changeset 2:b1e152172de9 (2016-12-06) Next changeset 4:2f41fac75575 (2016-12-07) |
Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 336e603ddd23f30f60f1cc40a4e8e1629d467055 |
modified:
lumpy.xml |
b |
diff -r b1e152172de9 -r 0bd777f0d6d8 lumpy.xml --- a/lumpy.xml Tue Dec 06 17:29:34 2016 -0500 +++ b/lumpy.xml Wed Dec 07 05:26:21 2016 -0500 |
b |
@@ -30,7 +30,7 @@ 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 $seq_method.additional_params.tt - -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$seq_method.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:$seq_method.additional_params.min_mapping_threshold + -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$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 && mv input.splitters.bam $splits && @@ -68,8 +68,8 @@ 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 $seq_method.additional_params.tt - -pe id:inputA.bam,bam_file:input.A.discordants.bam,histo_file:input.A.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$seq_method.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:$seq_method.additional_params.min_mapping_threshold - -pe id:inputB.bam,bam_file:input.B.discordants.bam,histo_file:input.B.lib.histo,mean:"\$meanB",stdev:"\$stdevA",read_length:$seq_method.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:$seq_method.additional_params.min_mapping_threshold + -pe id:inputA.bam,bam_file:input.A.discordants.bam,histo_file:input.A.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$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 -sr id:inputB.bam,bam_file:input.B.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.A.discordants.bam $discordants && @@ -99,16 +99,19 @@ <!-- basic error handling --> <inputs> <conditional name="analysis_type"> - <param help="Single or paired conditions (eg tumor vs normal)" label="Analysis type" name="analysis_type_list" type="select"> + <param help="Single or paired conditions (eg tumor vs normal)" label="Input(s)" name="analysis_type_list" type="select"> <option selected="True" value="one_sample">One Sample</option> <option value="two_sample">Two samples</option> </param> <when value="one_sample"> <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/> + <param name="readLength" value="151" type="integer" label="read length" help="e.g. 151 nt" /> </when> <when value="two_sample"> <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/> + <param name="readLength" value="151" type="integer" label="read length" help="e.g. 151 nt" /> <param format="bam" name="input_fileB" type="data" label="One BAM alignment file produced by BWA-mem"/> + <param name="readLengthB" value="151" type="integer" label="read length" help="e.g. 151 nt" /> </when> </conditional> <conditional name="seq_method"> @@ -117,7 +120,6 @@ <option value="single-read">Single-read sequencing</option> </param> <when value="paired-end"> - <param name="readLength" value="151" type="integer" label="read length" help="e.g. 151 nt" /> <section name="additional_params" title="Additional Options" expanded="False"> <param name="samplingValue" value="100000" type="integer" label="number of reads to compute mean and stdev of read length" help="e.g. 10000" /> <param name="mw" value="4" type="integer" label="-mw" help="minimum weight across all samples for a call (default: 4)" /> @@ -181,6 +183,26 @@ <help> +**Input(s)** + +*One sample* : lumpy search structural variations inside a single sequencing dataset + +*Two samples*: lumpy search structural variations inside and across two sequencing datasets from two samples + +Analysis of sample replicates is not implemented yet in this wrapper + +*BAM files*: Only BAM alignments produced by BWA-mem have been tested with this tool + +**Sequencing method** + +*Paired-end sequencing*: Both ends of library fragments have been sequenced, resulting in two paired sequencing datasets + +*Single-read sequencing*: Only one end of library fragment has been sequenced, resulting in a single sequencing dataset. Under these conditions, evidences of structural variation are obtained only from splited read alignments + +*Read length*: The length of the sequencing reads in the library. This information is required only for paired-end sequencing data + +*Additional options*: refer to lumpy-sv_ documentation and the publication (doi 10.1186/gb-2014-15-6-r84) + **lumpy-sv manual** Read the lumpy-sv_ documentation for details on using lumpy. |