Mercurial > repos > blankenberglab > data_manager_refgenie_pull

comparison data_manager/data_manager_refgenie_pull.xml @ 0:aec9bc48cdb7 draft

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"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
author blankenberglab
date Fri, 10 Sep 2021 12:56:54 +0000
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children 43d2baff05cd
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-1:000000000000 0:aec9bc48cdb7
1 <tool id="data_manager_refgenie_pull" name="refgenie asset pulling" version="@VERSION@" tool_type="manage_data" profile="20.05">
2 <description>from remote resource</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@VERSION@">refgenie</requirement>
8 </requirements>
9 <code file="data_manager_refgenie_pull.py" />
10 <environment_variables>
11 <environment_variable name="API_KEY" inject="api_key" />
12 </environment_variables>
13 <command detect_errors="exit_code"><![CDATA[
14 #for $asset in $assets:
15 #set ga = str($asset).split('/',2)
16 refgenie pull -c '$__app__.config.refgenie_config_file' -g '$ga[1]' '$ga[2]' $force >> '${out_log}' 2>&1
17 &&
18 #end for
19 echo '{}' > '${out_file}'
20 #if $api_refresh:
21 && python '${__tool_directory__}/data_manager_refgenie_pull.py' -k "\$API_KEY" -u '${__galaxy_url__}' >> '${out_log}'
22 #end if
23 ]]></command>
24 <inputs>
25 <param argument="--assets" name="assets" type="drill_down" display="checkbox" hierarchy="exact" multiple="True" optional="False" label="Select desired asset" dynamic_options="galaxy_code_get_refgenie_assets(__trans__.app.config.refgenie_config_file)" help="string of asset-registry-paths">
26 <validator type="regex" message="You must select an asset, not the remote URL or genome.">.+/.+/.+</validator>
27 </param>
28 <param argument="--force" name="force" type="boolean" truevalue="--force" falsevalue="" checked="False" label="Force (re-)download" />
29 <param argument="--api_refresh" name="api_refresh" type="boolean" truevalue="--api_refresh" falsevalue="" checked="True" label="Refresh Galaxy data tables using API" />
30 </inputs>
31 <outputs>
32 <data name="out_file" format="data_manager_json"/>
33 <data name="out_log" format="txt"/>
34 </outputs>
35 <tests>
36 <test>
37 <param name="assets" value="aHR0cDovL3JlZmdlbm9tZXMuZGF0YWJpby5vcmcvdjIvYXNzZXRz/t7/fasta:default"/>
38 <param name="force" value="--force"/>
39 <param name="api_refresh" value=""/>
40 <output name="out_file">
41 <assert_contents>
42 <has_text text="{}"/>
43 </assert_contents>
44 </output>
45 <output name="out_log">
46 <assert_contents>
47 <has_text text="Download complete"/>
48 </assert_contents>
49 </output>
50 </test>
51 </tests>
52 <help><![CDATA[
53 **What it does**
54
55 Fetches a reference genome using refgenie (http://refgenie.databio.org).
56
57 .. class:: infomark
58
59 **Notice:** Galaxy data tables will be refreshed using API calls.
60
61 .. class:: warning
62
63 **You must configure Galaxy to use refgenie, by setting 'refgenie_config_file' in the Galaxy config. This tool uses refgenie config file version 0.3.**
64 ]]></help>
65 <citations>
66 <citation type="doi">10.1093/gigascience/giz149</citation>
67 <citation type="doi">10.1101/2020.10.09.327114</citation>
68 </citations>
69 </tool>