Mercurial > repos > greg > vsnp_determine_ref_from_data
changeset 5:77eb4c46ee88 draft
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_determine_ref_from_data commit fab4644851280deb554f15f4b5f4770f8700e2c2"
| author | greg |
|---|---|
| date | Wed, 16 Jun 2021 16:54:04 +0000 |
| parents | 36bdf8b439ed |
| children | 09c5711c0221 |
| files | .shed.yml test-data/CMC_20E1_R1.fastq.gz test-data/CMC_20E1_R2.fastq.gz test-data/Mcap_Deer_DE_SRR650221.fastq.gz test-data/NC_002945v4.yml test-data/output_dbkey.txt test-data/output_metrics.txt test-data/paired_collection_metrics.txt test-data/paired_dbkey.txt test-data/paired_metrics.txt test-data/vsnp_dnaprints.loc tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 13 files changed, 45 insertions(+), 11 deletions(-) [+] |
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--- a/.shed.yml Sun Jan 03 16:13:22 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -name: vsnp_determine_ref_from_data -owner: greg -description: | - Contains a tool that sniffs bacterial genome samples to discover the primary species within the sample. -homepage_url: https://github.com/USDA-VS/vSNP -long_description: | - Contains a tool that sniffs bacterial genome samples to discover the primary species within the sample. -remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_determine_ref_from_data -type: unrestricted -categories: - - Sequence Analysis
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_002945v4.yml Wed Jun 16 16:54:04 2021 +0000 @@ -0,0 +1,5 @@ +bovis: + - '11001110' + - '11011110' + - '11001100' +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_dbkey.txt Wed Jun 16 16:54:04 2021 +0000 @@ -0,0 +1,1 @@ +AF2122 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_metrics.txt Wed Jun 16 16:54:04 2021 +0000 @@ -0,0 +1,6 @@ +Sample: Mcap_Deer_DE_SRR650221_fastq_gz +Brucella counts: 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, +TB counts: 2,2,0,0,4,5,0,0, +Para counts: 0,0,0, +Group: TB +dbkey: AF2122
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_collection_metrics.txt Wed Jun 16 16:54:04 2021 +0000 @@ -0,0 +1,6 @@ +Sample: CMC_20E1_R1_fastq_gz +Brucella counts: 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, +TB counts: 4,4,0,0,8,10,0,0, +Para counts: 0,0,0, +Group: TB +dbkey: AF2122
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_dbkey.txt Wed Jun 16 16:54:04 2021 +0000 @@ -0,0 +1,1 @@ +AF2122 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_metrics.txt Wed Jun 16 16:54:04 2021 +0000 @@ -0,0 +1,6 @@ +Sample: CMC_20E1_R1_fastq_gz +Brucella counts: 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, +TB counts: 4,4,0,0,8,10,0,0, +Para counts: 0,0,0, +Group: TB +dbkey: AF2122
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vsnp_dnaprints.loc Wed Jun 16 16:54:04 2021 +0000 @@ -0,0 +1,5 @@ +## vSNP DNAprints files +#Value Name Path Description +AF2122 Mycobacterium_AF2122/NC_002945v4.yml ${__HERE__}/NC_002945v4.yml DNAprints file for Mycobacterium bovis AF2122/97 +#NC_006932 Brucella_abortus1/NC_006932-NC_006933.yml /vsnp/NC_006932/Brucella_abortus1/NC_006932-NC_006933.yml DNAprints file for Brucella abortus bv. 1 str. 9-941 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Jun 16 16:54:04 2021 +0000 @@ -0,0 +1,8 @@ +<tables> + <!-- Location of dnaprints files for vsnp_dtermine_ref_from_data tool --> + <table name="vsnp_dnaprints" comment_char="#"> + <columns>value, name, path, description</columns> + <file path="tool-data/vsnp_dnaprints.loc" /> + </table> +</tables> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Jun 16 16:54:04 2021 +0000 @@ -0,0 +1,7 @@ +<tables> + <table name="vsnp_dnaprints" comment_char="#"> + <columns>value, name, path, description</columns> + <file path="${__HERE__}/test-data/vsnp_dnaprints.loc" /> + </table> +</tables> +