Mercurial > repos > greg > data_manager_vsnp_genbank
view data_manager/vsnp_genbank_fetcher.xml @ 2:df67ba6db5de draft default tip
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author | greg |
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date | Wed, 06 May 2020 10:58:29 -0400 |
parents | f1a7a3faaf3d |
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<?xml version="1.0"?> <tool id="vsnp_genbank_fetcher" name="vSNP Genbank data manager" tool_type="manage_data" profile="18.09" version="0.0.8"> <description>Download vSNP Genbank files</description> <requirements> <requirement type="package" version="3.7">python</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/vsnp_genbank_fetcher.py' --dbkey '${all_fasta_source.fields.dbkey}' --name '${all_fasta_source.fields.name}' --out_file '$out_file' --url '$url' ]]> </command> <inputs> <param name="all_fasta_source" type="select" label="FASTA reference"> <options from_data_table="all_fasta"/> </param> <param name="url" type="text" value="" label="URL to download the Genbank file associated with the selected FASTA reference" optional="False" /> </inputs> <outputs> <data name="out_file" format="data_manager_json" /> </outputs> <tests> <test> <param name="all_fasta_source" value="AF2122"/> <param name="url" value="https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/NC_002945v4.gbk"/> <output name="out_file" value="vsnp_genbank.json" compare="contains"/> </test> </tests> <help><![CDATA[ This tool fetches a vSNP Genbank file associated with each supported genome reference to populate the vsnp_genbank data table. The dbkey and name fields in the vsnp data table are inherited from the *all_fasta* data table, so no user entry is necessary. These public vSNP Genbank files are available in GitHub at https://github.com/USDA-VS/vSNP_reference_options. * **Mycobacterium bovis AF2122/97** * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/NC_002945v4.gbk * **Brucella abortus bv. 1 str. 9-941** * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus1/NC_006932-NC_006933.gbk * **Brucella abortus strain BER** * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/NZ_CP007682-NZ_CP007683.gbk * **Brucella canis ATCC 23365** * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/NC_010103-NC_010104.gbk * **Brucella ceti TE10759-12** * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/NC_022905-NC_022906.gbk * **Brucella melitensis bv. 1 str. 16M** * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/NC_003317-NC_003318.gbk * **Brucella melitensis bv. 3 str. Ether** * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/NZ_CP007760-NZ_CP007761.gbk * **Brucella melitensis BwIM_SOM_36b** * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/NZ_CP018508-NZ_CP018509.gbk * **Brucella melitensis ATCC 23457** * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/NC_012441-NC_012442.gbk * **Brucella ovis ATCC 25840** * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/NC_009505-NC_009504.gbk * **Brucella suis 1330** * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/NC_017251-NC_017250.gbk * **Mycobacterium tuberculosis H37Rv** * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/NC_000962.gbk * **Mycobacterium avium subsp. paratuberculosis strain Telford** * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-CP033688/CP033688.gbk * **Mycobacterium avium subsp. paratuberculosis K-10** * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-NC002944/NC_002944.gbk * **Brucella suis ATCC 23445** * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/NC_010169-NC_010167.gbk * **Brucella suis bv. 3 str. 686** * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/NZ_CP007719-NZ_CP007718.gbk ]]></help> <citations> </citations> </tool>