Mercurial > repos > iuc > data_manager_fetch_refseq

comparison data_manager/fetch_refseq.xml @ 2:f0b1b5b4d227 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
author iuc
date Thu, 28 Nov 2019 20:30:26 +0000
parents 4eb858aa879c
children 4314700c39d5
comparison
equal deleted inserted replaced
1:4eb858aa879c 2:f0b1b5b4d227
1 <tool id="data_manager_fetch_refseq" name="RefSeq data manager" version="0.0.18" tool_type="manage_data"> 1 <tool id="data_manager_fetch_refseq" name="RefSeq data manager" version="0.0.19" tool_type="manage_data" profile="19.05">
2 <description>Fetch FASTA data from NCBI RefSeq and update all_fasta data table</description> 2 <description>Fetch FASTA data from NCBI RefSeq and update all_fasta data table</description>
3 <requirements> 3 <requirements>
4 <requirement type="package">python</requirement> 4 <requirement type="package" version="3.7">python</requirement>
5 <requirement type="package">requests</requirement> 5 <requirement type="package" version="2.22.0">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}
63 <param name="advanced_selector" value="basic"/> 63 <param name="advanced_selector" value="basic"/>
64 <output name="output_file"> 64 <output name="output_file">
65 <assert_contents> 65 <assert_contents>
66 <has_text text="2018-03-14"/> 66 <has_text text="2018-03-14"/>
67 <has_text text="refseq_plastid"/> 67 <has_text text="refseq_plastid"/>
68 <has_text text="/refseq_plastid."/>
69 </assert_contents> 68 </assert_contents>
70 </output> 69 </output>
71 </test> 70 </test>
72 <test> 71 <test>
73 <param name="division_names" value="plastid"/> 72 <param name="division_names" value="plastid"/>
77 <param name="compress" value="" /> 76 <param name="compress" value="" />
78 <output name="output_file"> 77 <output name="output_file">
79 <assert_contents> 78 <assert_contents>
80 <has_text text="2018-03-14"/> 79 <has_text text="2018-03-14"/>
81 <has_text text="refseq_plastid"/> 80 <has_text text="refseq_plastid"/>
82 <has_text text="/refseq_plastid."/>
83 </assert_contents> 81 </assert_contents>
84 </output> 82 </output>
85 </test> 83 </test>
86 84
87 </tests> 85 </tests>