| Previous changeset 1:a006d42dd759 (2016-12-06) Next changeset 3:0bd777f0d6d8 (2016-12-07) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241 |
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modified:
lumpy.xml |
| b |
| diff -r a006d42dd759 -r b1e152172de9 lumpy.xml --- a/lumpy.xml Tue Dec 06 09:29:31 2016 -0500 +++ b/lumpy.xml Tue Dec 06 17:29:34 2016 -0500 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="lumpy" name="lumpy-sv" version="0.1">\n+<tool id="lumpy" name="lumpy-sv" version="0.2">\n <description>find structural variants</description>\n <requirements>\n <requirement type="package" version="0.2.12">lumpy-sv</requirement>\n@@ -10,38 +10,107 @@\n </stdio>\n <version_command>lumpy --version</version_command>\n <command><![CDATA[\n- ln -f -s "$input_file" input.bam &&\n- #if $seq_method.seq_method_list == "paired-end":\n- samtools view -b -F 1294 input.bam > "input.discordants.unsorted.bam" &&\n- samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" &&\n- samtools sort input.discordants.unsorted.bam > input.discordants.bam &&\n- samtools sort input.splitters.unsorted.bam > input.splitters.bam &&\n- samtools view -r readgroup input.bam\n- |tail -n +$seq_method.additional_params.samplingValue\n- |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt &&\n- mean=\\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) &&\n- stdev=\\$(cat meandev.txt | sed -r s/mean:.+stdev://) &&\n- lumpy -mw 4 -tt 0 \n- -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 \n- -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 &&\n- mv input.discordants.bam $discordants &&\n- mv input.splitters.bam $splits &&\n- mv input.lib.histo $histogram &&\n- mv output.vcf $vcf_call &&\n- rm input.discordants.unsorted.bam input.splitters.unsorted.bam meandev.txt\n+ #if $analysis_type.analysis_type_list == "one_sample":\n+ ln -f -s $analysis_type.input_file input.bam &&\n+ #else:\n+ ln -f -s $analysis_type.input_file input.A.bam &&\n+ ln -f -s $analysis_type.input_fileB input.B.bam &&\n #end if\n- #if $seq_method.seq_method_list == "single-read":\n- samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" &&\n- lumpy -mw 4 -tt 0\n- -sr id:input.bam,bam_file:input.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf &&\n- mv input.splitters.unsorted.bam $splits &&\n- mv output.vcf $vcf_call\n+\n+ #if $analysis_type.analysis_type_list == "one_sample":\n+\n+ #if $seq_method.seq_method_list == "paired-end":\n+ samtools view -b -F 1294 input.bam > "input.discordants.unsorted.bam" &&\n+ samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" &&\n+ samtools sort input.discordants.unsorted.bam > input.discordants.bam &&\n+ samtools sort input.splitters.unsorted.bam > input.splitters.bam &&\n+ samtools view -r readgroup input.bam\n+ |tail -n +$seq_method.additional_params.samplingValue\n+ |python $__tool_directory__/pairend_distro.py -r'..b'\n+ <param name="tt" value="0" type="integer" label="-tt" help="trim threshold (default: 0)" />\n <param name="min_non_overlap" value="101" type="integer" label="min_non_overlap" help="e.g. 101" />\n <param name="discordant_z" value="5" type="integer" label="discordant_z" help="e.g. 5" />\n <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" />\n@@ -60,6 +131,8 @@\n </when>\n <when value="single-read">\n <section name="additional_params" title="Additional Options" expanded="False">\n+ <param name="mw" value="4" type="integer" label="-mw" help="minimum weight across all samples for a call (default: 4)" />\n+ <param name="tt" value="0" type="integer" label="-tt" help="trim threshold (default: 0)" />\n <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" />\n <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" />\n <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" />\n@@ -71,20 +144,34 @@\n </inputs>\n \n <outputs>\n- <data format="tabular" name="histogram" type="data" label="Lumpy on ${input_file.element_identifier}: Fragment size distribution">\n+ <data format="tabular" name="histogram" type="data" label="Lumpy on ${analysis_type.input_file.element_identifier}: Fragment size distribution">\n <filter>seq_method[\'seq_method_list\'] == "paired-end"</filter>\n </data>\n- <data format="bam" name="splits" type="data" label="Lumpy on ${input_file.element_identifier}: Split Reads (Bam format)"/>\n- <data format="bam" name="discordants" type="data" label="Lumpy on ${input_file.element_identifier}: Discordant Pairs (Bam format)">\n+ <data format="tabular" name="histogramB" type="data" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Fragment size distribution">\n+ <filter>seq_method[\'seq_method_list\'] == "paired-end"</filter>\n+ <filter>analysis_type[\'analysis_type_list\'] == "two_sample"</filter>\n+ </data>\n+ <data format="bam" name="splits" type="data" label="Lumpy on ${analysis_type.input_file.element_identifier}: Split Reads (Bam format)"/>\n+ <data format="bam" name="splitsB" type="data" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Split Reads (Bam format)">\n+ <filter>analysis_type[\'analysis_type_list\'] == "two_sample"</filter>\n+ </data>\n+ <data format="bam" name="discordants" type="data" label="Lumpy on ${analysis_type.input_file.element_identifier}: Discordant Pairs (Bam format)">\n <filter>seq_method[\'seq_method_list\'] == "paired-end"</filter>\n </data>\n- <data format="vcf" name="vcf_call" type="data" label="Lumpy on ${input_file.element_identifier}: Variant Calling (vcf format)"/>\n+ <data format="bam" name="discordantsB" type="data" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Discordant Pairs (Bam format)">\n+ <filter>seq_method[\'seq_method_list\'] == "paired-end"</filter>\n+ <filter>analysis_type[\'analysis_type_list\'] == "two_sample"</filter>\n+ </data>\n+ <data format="vcf" name="vcf_call" type="data" label="Lumpy Variant Calling (vcf format)"/>\n </outputs>\n \n <tests>\n <test>\n+ <param name="analysis_type" value="one_sample" />\n <param name="input_file" value="sr.input.bam" ftype="bam"/>\n <param name="seq_method_list" value="single-read" />\n+ <param name="mw" value="4"/>\n+ <param name="tt" value="0"/>\n <param name="back_distance" value="10"/>\n <param name="weight" value="1" />\n <param name="min_mapping_threshold" value="20" />\n' |