Mercurial > repos > drosofff > lumpy
changeset 4:2f41fac75575 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 66d42b0d63ff5d72c6611106ed3366a58c73a55d
| author | drosofff |
|---|---|
| date | Wed, 07 Dec 2016 09:52:03 -0500 |
| parents | 0bd777f0d6d8 |
| children | 745cbe841e40 |
| files | lumpy.xml |
| diffstat | 1 files changed, 10 insertions(+), 10 deletions(-) [+] |
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--- a/lumpy.xml Wed Dec 07 05:26:21 2016 -0500 +++ b/lumpy.xml Wed Dec 07 09:52:03 2016 -0500 @@ -25,7 +25,7 @@ samtools sort input.discordants.unsorted.bam > input.discordants.bam && samtools sort input.splitters.unsorted.bam > input.splitters.bam && samtools view -r readgroup input.bam - |tail -n +$seq_method.additional_params.samplingValue + |tail -n +1 |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt && mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) && stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) && @@ -58,10 +58,10 @@ samtools sort input.A.splitters.unsorted.bam > input.A.splitters.bam && samtools sort input.B.splitters.unsorted.bam > input.B.splitters.bam && samtools view -r readgroup input.A.bam - |tail -n +$seq_method.additional_params.samplingValue + |tail -n +1 |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.A.lib.histo > meandevA.txt && samtools view -r readgroup input.B.bam - |tail -n +$seq_method.additional_params.samplingValue + |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 && meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) && meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) && @@ -146,25 +146,25 @@ </inputs> <outputs> - <data format="tabular" name="histogram" type="data" label="Lumpy on ${analysis_type.input_file.element_identifier}: Fragment size distribution"> + <data format="tabular" name="histogram" label="Lumpy on ${analysis_type.input_file.element_identifier}: Fragment size distribution"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> </data> - <data format="tabular" name="histogramB" type="data" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Fragment size distribution"> + <data format="tabular" name="histogramB" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Fragment size distribution"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> </data> - <data format="bam" name="splits" type="data" label="Lumpy on ${analysis_type.input_file.element_identifier}: Split Reads (Bam format)"/> - <data format="bam" name="splitsB" type="data" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Split Reads (Bam format)"> + <data format="bam" name="splits" label="Lumpy on ${analysis_type.input_file.element_identifier}: Split Reads (Bam format)"/> + <data format="bam" name="splitsB" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Split Reads (Bam format)"> <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> </data> - <data format="bam" name="discordants" type="data" label="Lumpy on ${analysis_type.input_file.element_identifier}: Discordant Pairs (Bam format)"> + <data format="bam" name="discordants" label="Lumpy on ${analysis_type.input_file.element_identifier}: Discordant Pairs (Bam format)"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> </data> - <data format="bam" name="discordantsB" type="data" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Discordant Pairs (Bam format)"> + <data format="bam" name="discordantsB" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Discordant Pairs (Bam format)"> <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" type="data" label="Lumpy Variant Calling (vcf format)"/> + <data format="vcf" name="vcf_call" label="Lumpy Variant Calling (vcf format)"/> </outputs> <tests>