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comparison lumpy.xml @ 11:ecbc563571ea draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 079a105fb5e798410bfae15590daa79163d885ad
author drosofff
date Mon, 12 Dec 2016 13:45:08 -0500
parents 4584440b2634
children b3fb23bbca8e
comparison
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10:4584440b2634 11:ecbc563571ea
70 |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLengthB -X 4 -N $seq_method.additional_params.samplingValue -o input.B.lib.histo > meandevB.txt && 70 |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLengthB -X 4 -N $seq_method.additional_params.samplingValue -o input.B.lib.histo > meandevB.txt &&
71 meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) && 71 meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
72 meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) && 72 meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
73 stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) && 73 stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) &&
74 stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) && 74 stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) &&
75 <<<<<<< HEAD
76 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt 75 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
77 #if $output_format == "BEDPE": 76 #if $output_format == "BEDPE":
78 -b 77 -b
79 #end if 78 #end if
80 -pe id:inputA.bam,bam_file:input.A.discordants.bam,histo_file:input.A.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$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:$seq_method.additional_params.min_mapping_threshold 79 -pe id:inputA.bam,bam_file:input.A.discordants.bam,histo_file:input.A.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$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