Mercurial > repos > hepcat72 > lumpyexpress
comparison lumpyexpress.xml @ 1:107fa8e0b744 draft
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 461cce84aa93505ac05547a2a28865ff8c0dfefb
| author | hepcat72 |
|---|---|
| date | Tue, 16 Oct 2018 17:34:40 -0400 |
| parents | e5150e64206a |
| children | bfd745cf84c2 |
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| 0:e5150e64206a | 1:107fa8e0b744 |
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| 1 <tool id="lumpyexpress_0_1" name="lumpyexpress" version="0.1.0"> | 1 <tool id="lumpyexpress_0_1" name="lumpyexpress" version="0.1.1"> |
| 2 <description>Single or paired end SV detection</description> | 2 <description>Single or paired end SV detection</description> |
| 3 | 3 |
| 4 <requirements> | 4 <requirements> |
| 5 <requirement type="package" version="2.7">python</requirement> | 5 <requirement type="package" version="2.7">python</requirement> |
| 6 <requirement type="package" version="0.8.3">pysam</requirement> | 6 <requirement type="package" version="0.8.3">pysam</requirement> |
| 7 <requirement type="package" version="1.13.1">numpy</requirement> | 7 <requirement type="package" version="1.13.1">numpy</requirement> |
| 8 <requirement type="package" version="0.2.14a">lumpy-sv</requirement> | 8 <requirement type="package" version="0.2.13">lumpy-sv</requirement> |
| 9 <requirement type="package" version="1.9">samtools</requirement> | 9 <requirement type="package" version="1.9">samtools</requirement> |
| 10 <requirement type="package" version="0.1.24">samblaster</requirement> | 10 <requirement type="package" version="0.1.24">samblaster</requirement> |
| 11 <requirement type="package" version="0.6.5">sambamba</requirement> | 11 <requirement type="package" version="0.6.5">sambamba</requirement> |
| 12 <requirement type="package" version="4.2.1">gawk</requirement> | 12 <requirement type="package" version="4.2.1">gawk</requirement> |
| 13 </requirements> | 13 </requirements> |
| 14 | 14 |
| 15 <version_command>___COMMAND___ ___VERSION_FLAG___</version_command> | 15 <version_command>lumpy --version</version_command> |
| 16 | 16 |
| 17 <command detect_errors="aggressive"> | 17 <command detect_errors="aggressive"> |
| 18 <![CDATA[ | 18 <![CDATA[ |
| 19 $__tool_directory__/lumpy_wrapper.tcsh | 19 $__tool_directory__/lumpy_wrapper.tcsh |
| 20 '$paired' | 20 '$paired' |
| 62 <help> | 62 <help> |
| 63 <![CDATA[ | 63 <![CDATA[ |
| 64 Paired-end data is processed with lumpyexpress using only the required arguments. Single-end data is processed with lumpy using `-mw 4 -tt 0 -sr id:<SAMPLE>,bam_file:<SAMPLE>.splitters.bam,back_distance:10,weight:1,min_mapping_threshold:20`. Submit an issue to the tool wrapper repo if you would like more options to be available: https://github.com/hepcat72/robs_galaxy_tools | 64 Paired-end data is processed with lumpyexpress using only the required arguments. Single-end data is processed with lumpy using `-mw 4 -tt 0 -sr id:<SAMPLE>,bam_file:<SAMPLE>.splitters.bam,back_distance:10,weight:1,min_mapping_threshold:20`. Submit an issue to the tool wrapper repo if you would like more options to be available: https://github.com/hepcat72/robs_galaxy_tools |
| 65 | 65 |
| 66 Split reads and discordant reads are extracted from the supplied bam files. Each bam file should represent a different sample. | 66 Split reads and discordant reads are extracted from the supplied bam files. Each bam file should represent a different sample. |
| 67 | |
| 68 This is a wrapper for lumpyexpress that comes with lumpy-sv version 0.2.13. The script in the latest version of lumpy-sv (0.2.14a) has some issues when run on galaxy. | |
| 67 ]]> | 69 ]]> |
| 68 </help> | 70 </help> |
| 69 | 71 |
| 70 <citations> | 72 <citations> |
| 71 <citation type="doi">10.1186/gb-2014-15-6-r84</citation> | 73 <citation type="doi">10.1186/gb-2014-15-6-r84</citation> |