| Previous changeset 7:e833b178b94b (2016-12-09) Next changeset 9:43462e6e9140 (2016-12-12) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 8375ddf784506b68d28bc9e6224648fafa796d9f |
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modified:
lumpy.xml |
| b |
| diff -r e833b178b94b -r 382ffb8e0caa lumpy.xml --- a/lumpy.xml Fri Dec 09 06:13:27 2016 -0500 +++ b/lumpy.xml Sat Dec 10 20:26:56 2016 -0500 |
| [ |
| b'@@ -8,7 +8,6 @@\n <stdio>\n <exit_code range="1:" level="fatal" description="Tool exception" />\n </stdio>\n- <version_command>lumpy --version</version_command>\n <command detect_errors="exit_code"><![CDATA[\n #if $analysis_type.analysis_type_list == "one_sample":\n ln -f -s \'$analysis_type.input_file\' input.bam &&\n@@ -24,16 +23,16 @@\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+ samtools view input.bam\n |tail -n +1\n- |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt &&\n+ |python $__tool_directory__/pairend_distro.py -r $readLength -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 $seq_method.additional_params.mw -tt $seq_method.additional_params.tt\n #if $output_format == "BEDPE":\n -b\n #end if\n- -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\\$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 \n+ -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\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@@ -51,7 +50,7 @@\n mv input.splitters.unsorted.bam $splits &&\n mv output.vcf $vcf_call\n #end if\n- \n+\n #else:\n \n #if $seq_method.seq_method_list == "paired-end":\n@@ -63,22 +62,23 @@\n samtools sort input.B.discordants.unsorted.bam > input.B.discordants.bam &&\n samtools sort input.A.splitters.unsorted.bam > input.A.splitters.bam &&\n samtools sort input.B.splitters.unsorted.bam > input.B.splitters.bam &&\n- samtools view -r readgroup input.A.bam\n+ samtools view input.A.bam\n |tail -n +1\n- |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.A.lib.histo > meandevA.txt &&\n- samtools view -r readgroup input.B.bam\n+ |python $__tool_directory__/pairend_distro.py -r $readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.A.lib.histo > meandevA.txt &&\n+ samtools view input.B.bam\n |tail -n +1\n- |python $__tool_directory__/p'..b' lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt \n+<<<<<<< HEAD\n+ lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt\n #if $output_format == "BEDPE":\n -b\n #end if\n- -pe id:inputA.bam,bam_file:input.A.discordants.bam,histo_file:input.A.lib.histo,mean:"\\$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 \n- -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 \n+ -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\n+ -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\n -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:$seq_method.additional_params.min_mapping_threshold\n -sr id:inputB.bam,bam_file:input.B.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf &&\n mv input.A.discordants.bam $discordants &&\n@@ -104,7 +104,7 @@\n mv output.vcf $vcf_call\n #end if\n \n- \n+\n #end if\n \n ]]></command>\n@@ -152,7 +152,7 @@\n <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" />\n </section>\n </when>\n- \n+\n </conditional>\n <param help="get variant calling in vcf or BEDPE format" label="variant calling format" name="output_format" type="select">\n <option selected="True" value="vcf">vcf</option>\n@@ -201,7 +201,7 @@\n </tests>\n \n <help>\n- \n+\n **Input(s)**\n \n *One sample* : lumpy search structural variations inside a single sequencing dataset\n@@ -221,7 +221,7 @@\n *Read length*: The length of the sequencing reads in the library. This information is required only for paired-end sequencing data\n \n *Additional options*: refer to lumpy-sv_ documentation and the publication (doi 10.1186/gb-2014-15-6-r84)\n- \n+\n **lumpy-sv manual**\n \n Read the lumpy-sv_ documentation for details on using lumpy.\n@@ -271,8 +271,8 @@\n \n \t-bedpe\tbedpe_file:<bedpe file>,\n \t\tid:<sample name>,\n-\t\tweight:<sample weight> \n-]]>\t\t\n+\t\tweight:<sample weight>\n+]]>\n </help>\n \n <citations>\n' |