Mercurial > repos > iuc > data_manager_fetch_refseq
comparison data_manager/fetch_refseq.xml @ 1:937f167631b1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 8cad1e44b2393cb36f60a4d705536dee235a8434
author | iuc |
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date | Sun, 13 Jan 2019 09:26:57 -0500 |
parents | 8b91891ae805 |
children | 5d2ef93c6314 |
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0:8b91891ae805 | 1:937f167631b1 |
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5 <requirement type="package">requests</requirement> | 5 <requirement type="package">requests</requirement> |
6 </requirements> | 6 </requirements> |
7 <command detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
8 python $__tool_directory__/fetch_refseq.py | 8 python $__tool_directory__/fetch_refseq.py |
9 #if str( $advanced.advanced_selector ) == 'advanced': | 9 #if str( $advanced.advanced_selector ) == 'advanced': |
10 '${advanced.compress}' | 10 ${advanced.compress} |
11 #end if | 11 #end if |
12 --galaxy_datamanager_filename '${output_file}' | 12 --galaxy_datamanager_filename '${output_file}' |
13 --division_names ${division_names} | 13 --division_names ${division_names} |
14 --mol_types ${mol_types} | 14 --mol_types ${mol_types} |
15 #if str( $pin_date ) != 'NO': | 15 #if str( $pin_date ) != 'NO': |
67 <has_text text="refseq_plastid"/> | 67 <has_text text="refseq_plastid"/> |
68 <has_text text="/refseq_plastid."/> | 68 <has_text text="/refseq_plastid."/> |
69 </assert_contents> | 69 </assert_contents> |
70 </output> | 70 </output> |
71 </test> | 71 </test> |
72 <test> | |
73 <param name="division_names" value="plastid"/> | |
74 <param name="mol_types" value="protein"/> | |
75 <param name="pin_date" value="2018-03-14"/> | |
76 <param name="advanced_selector" value="advanced"/> | |
77 <param name="compress" value="" /> | |
78 <output name="output_file"> | |
79 <assert_contents> | |
80 <has_text text="2018-03-14"/> | |
81 <has_text text="refseq_plastid"/> | |
82 <has_text text="/refseq_plastid."/> | |
83 </assert_contents> | |
84 </output> | |
85 </test> | |
86 | |
72 </tests> | 87 </tests> |
73 <help><![CDATA[ | 88 <help><![CDATA[ |
74 This data manager fetches FASTA format collections of proteins, nucleotides (genomic DNA) and RNA | 89 This data manager fetches FASTA format collections of proteins, nucleotides (genomic DNA) and RNA |
75 from NCBI's RefSeq_ data collection. | 90 from NCBI's RefSeq_ data collection. |
76 | 91 |