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.shed.yml
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owner: "wolma"
remote_repository_url: "https://github.com/wm75/mimodd_galaxy_wrappers"
homepage_url: "mimodd.readthedocs.io"
categories:
- Variant Analysis
- SAM
- Next Gen Mappers
- Convert Formats
- Visualization
repositories:
mimodd_aln:
description: The MiModD Read Alignment tool
long_description: |
This tool provides access to the SNAP read aligner integrated into MiModD.
include:
- snap_caller.xml
- macros.xml
- tool_data_table_conf.xml.sample
- tool-data
- test-data
- COPYING
- LICENSE
mimodd_snpeff:
description: SnpEff-dependent functionality of MiModD
long_description: |
These tools require SnpEff installed and MiModD configured to use it.
They enable the annotation of variants identified with the MiModD core
tools with functional effects.
include:
- annotate_variants.xml
- snpeff_genomes.xml
- macros.xml
- COPYING
- LICENSE
mimodd_main:
description: The main tools of the MiModD suite of tools.
long_description: These tools provide the main mapping-by-sequencing
functionality of MiModD. Note that sequence reads have to be aligned to
the corresponding reference genome before they can be analyzed. This can
be done with any modern aligner of your choice or through the MiModD Read
Alignment tool available from the separate repository mimodd_aln.
Functional annotation of identified variants can be performed using
SnpEff. MiModD-specific wrappers for SnpEff are available from the
separate repository mimodd_snpeff though more general wrappers should be
compatible, too.
include:
- fileinfo.xml
- sam_header.xml
- convert.xml
- reheader.xml
- bamsort.xml
- snp_caller_caller.xml
- varextract.xml
- deletion_predictor.xml
- covstats.xml
- vcf_filter.xml
- rebase.xml
- varreport.xml
- cloudmap.xml
- macros.xml
- tool_data_table_conf.xml.sample
- tool-data
- test-data
- COPYING
- LICENSE
suite:
name: "suite_mimodd"
description: MiModD - A tool suite to identify mutations from whole-genome sequencing data
long_description: |
MiModD is an integrated solution for mapping-by-sequencing analysis of
whole-genome sequencing (WGS) data from laboratory model organisms. It
enables geneticists to identify the genetic variants underlying an observed
phenotype in a mutant organism starting from WGS read data. This suite
installs the full set of MiModD tools.
type: repository_suite_definition