Mercurial > repos > greg > data_manager_vsnp_dnaprints

comparison data_manager/vsnp_dnaprints_fetcher.xml @ 1:5c4173a0b2c6 draft

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author greg
date Tue, 05 May 2020 15:08:48 -0400
parents f58178a5eebc
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0:f58178a5eebc 1:5c4173a0b2c6
14 </command> 14 </command>
15 <inputs> 15 <inputs>
16 <param name="all_fasta_source" type="select" label="FASTA reference"> 16 <param name="all_fasta_source" type="select" label="FASTA reference">
17 <options from_data_table="all_fasta"/> 17 <options from_data_table="all_fasta"/>
18 </param> 18 </param>
19 <param name="url" type="text" value="" label="URL to download the DNAprints file associated with the selected FASTA reference" optional="False" /> 19 <param name="url" type="text" value="" label="URL to download the DNAprints file associated with the selected FASTA reference" optional="False"/>
20 </inputs> 20 </inputs>
21 <outputs> 21 <outputs>
22 <data name="out_file" format="data_manager_json" /> 22 <data name="out_file" format="data_manager_json"/>
23 </outputs> 23 </outputs>
24 <tests> 24 <tests>
25 <test> 25 <test>
26 <param name="all_fasta_source" value="AF2122"/>
27 <param name="url" value="https://raw.githubusercontent.com/USDA-VS/vSNP_reference_options/master/Mycobacterium_AF2122/NC_002945v4.yml"/>
28 <output name="out_file" value="vsnp_dnaprints.json" compare="contains"/>
26 </test> 29 </test>
27 </tests> 30 </tests>
28 <help><![CDATA[ 31 <help><![CDATA[
29 This tool fetches a vSNP DNAprints file associated with each supported genome reference to populate the vsnp_dnaprints data table. The dbkey and name fields 32 This tool fetches a vSNP DNAprints file associated with each supported genome reference to populate the vsnp_dnaprints data table. The dbkey and name fields
30 in the vsnp data table are inherited from the *all_fasta* data table, so no user entry is necessary. These public vSNP DNAprints files are available in GitHub 33 in the vsnp data table are inherited from the *all_fasta* data table, so no user entry is necessary. These public vSNP DNAprints files are available in GitHub