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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit bd0a0b0717fd7da2ff703668b21ff7db3677d61b |
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modified:
lumpy.xml |
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| diff -r 8b3daa745d9b -r a006d42dd759 lumpy.xml --- a/lumpy.xml Tue Dec 06 05:46:28 2016 -0500 +++ b/lumpy.xml Tue Dec 06 09:29:31 2016 -0500 |
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| @@ -71,14 +71,14 @@ </inputs> <outputs> - <data format="tabular" name="histogram" type="data" label="${input_file.element_identifier} Fragment size distribution"> + <data format="tabular" name="histogram" type="data" label="Lumpy on ${input_file.element_identifier}: Fragment size distribution"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> </data> - <data format="bam" name="splits" type="data" label="${input_file.element_identifier} Split Reads (Bam format)"/> - <data format="bam" name="discordants" type="data" label="${input_file.element_identifier} Discordant Pairs (Bam format)"> + <data format="bam" name="splits" type="data" label="Lumpy on ${input_file.element_identifier}: Split Reads (Bam format)"/> + <data format="bam" name="discordants" type="data" label="Lumpy on ${input_file.element_identifier}: Discordant Pairs (Bam format)"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> </data> - <data format="vcf" name="vcf_call" type="data" label="${input_file.element_identifier} Variant Calling (vcf format)"/> + <data format="vcf" name="vcf_call" type="data" label="Lumpy on ${input_file.element_identifier}: Variant Calling (vcf format)"/> </outputs> <tests> @@ -93,7 +93,57 @@ </tests> <help> - Some help required + +**lumpy-sv manual** + +Read the lumpy-sv_ documentation for details on using lumpy. + +.. _lumpy-sv: https://github.com/arq5x/lumpy-sv + +**lumpy options** + +v 0.2.13 +Author: Ryan Layer (rl6sf@virginia.edu) + +Summary: Find structural variations in various signals. + +Options:: + + -g Genome file (defines chromosome order) + -e Show evidence for each call + -w File read windows size (default 1000000) + -mw minimum weight for a call + -msw minimum per-sample weight for a call + -tt trim threshold + -x exclude file bed file + -t temp file prefix, must be to a writeable directory + -P output probability curve for each variant + -b output BEDPE instead of VCF + -sr bam_file:<file name>, + id:<sample name>, + back_distance:<distance>, + min_mapping_threshold:<mapping quality>, + weight:<sample weight>, + min_clip:<minimum clip length>, + read_group:<string> + + -pe bam_file:<file name>, + id:<sample name>, + histo_file:<file name>, + mean:<value>, + stdev:<value>, + read_length:<length>, + min_non_overlap:<length>, + discordant_z:<z value>, + back_distance:<distance>, + min_mapping_threshold:<mapping quality>, + weight:<sample weight>, + read_group:<string> + + -bedpe bedpe_file:<bedpe file>, + id:<sample name>, + weight:<sample weight> + </help> <citations> |