Mercurial > repos > drosofff > lumpy
diff lumpy.xml @ 8:382ffb8e0caa draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 8375ddf784506b68d28bc9e6224648fafa796d9f
| author | drosofff |
|---|---|
| date | Sat, 10 Dec 2016 20:26:56 -0500 |
| parents | e833b178b94b |
| children | 43462e6e9140 |
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--- a/lumpy.xml Fri Dec 09 06:13:27 2016 -0500 +++ b/lumpy.xml Sat Dec 10 20:26:56 2016 -0500 @@ -8,7 +8,6 @@ <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> </stdio> - <version_command>lumpy --version</version_command> <command detect_errors="exit_code"><![CDATA[ #if $analysis_type.analysis_type_list == "one_sample": ln -f -s '$analysis_type.input_file' input.bam && @@ -24,16 +23,16 @@ samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" && samtools sort input.discordants.unsorted.bam > input.discordants.bam && samtools sort input.splitters.unsorted.bam > input.splitters.bam && - samtools view -r readgroup input.bam + samtools view input.bam |tail -n +1 - |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt && + |python $__tool_directory__/pairend_distro.py -r $readLength -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 #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:$seq_method.additional_params.min_mapping_threshold + -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$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 && @@ -51,7 +50,7 @@ mv input.splitters.unsorted.bam $splits && mv output.vcf $vcf_call #end if - + #else: #if $seq_method.seq_method_list == "paired-end": @@ -63,22 +62,23 @@ samtools sort input.B.discordants.unsorted.bam > input.B.discordants.bam && samtools sort input.A.splitters.unsorted.bam > input.A.splitters.bam && samtools sort input.B.splitters.unsorted.bam > input.B.splitters.bam && - samtools view -r readgroup input.A.bam + samtools view input.A.bam |tail -n +1 - |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.A.lib.histo > meandevA.txt && - samtools view -r readgroup input.B.bam + |python $__tool_directory__/pairend_distro.py -r $readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.A.lib.histo > meandevA.txt && + samtools view input.B.bam |tail -n +1 - |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.B.lib.histo > meandevB.txt && + |python $__tool_directory__/pairend_distro.py -r $readLengthB -X 4 -N $seq_method.additional_params.samplingValue -o input.B.lib.histo > meandevB.txt && meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) && - meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) && + meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) && 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 +<<<<<<< HEAD + 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:$seq_method.additional_params.min_mapping_threshold + -pe id:inputA.bam,bam_file:input.A.discordants.bam,histo_file:input.A.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$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 && @@ -104,7 +104,7 @@ mv output.vcf $vcf_call #end if - + #end if ]]></command> @@ -152,7 +152,7 @@ <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" /> </section> </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> @@ -201,7 +201,7 @@ </tests> <help> - + **Input(s)** *One sample* : lumpy search structural variations inside a single sequencing dataset @@ -221,7 +221,7 @@ *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. @@ -271,8 +271,8 @@ -bedpe bedpe_file:<bedpe file>, id:<sample name>, - weight:<sample weight> -]]> + weight:<sample weight> +]]> </help> <citations>