Mercurial > repos > blankenberglab > data_manager_refgenie_pull

comparison data_manager/data_manager_refgenie_pull.xml @ 3:b2fa406276e7 draft default tip

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"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
author blankenberglab
date Fri, 01 Apr 2022 16:14:13 +0000
parents 43d2baff05cd
children
comparison
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2:2cb1863cd236 3:b2fa406276e7
1 <tool id="data_manager_refgenie_pull" name="refgenie asset pulling" version="@VERSION@" tool_type="manage_data" profile="20.05"> 1 <tool id="data_manager_refgenie_pull" name="refgenie asset pulling" version="@VERSION@+galaxy0" tool_type="manage_data" profile="20.05">
2 <description>from remote resource</description> 2 <description>from remote resource</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
16 #set ga = str($asset).split('/',2) 16 #set ga = str($asset).split('/',2)
17 refgenie pull -c '$__app__.config.refgenie_config_file' -g '$ga[1]' '$ga[2]' $force >> '${out_log}' 2>&1 17 refgenie pull -c '$__app__.config.refgenie_config_file' -g '$ga[1]' '$ga[2]' $force >> '${out_log}' 2>&1
18 && 18 &&
19 #end for 19 #end for
20 echo '{}' > '${out_file}' 20 echo '{}' > '${out_file}'
21 #if $api_refresh: 21 #if "refresh" in $str($api_refresh):
22 && python '${__tool_directory__}/data_manager_refgenie_pull.py' -k "\$API_KEY" -u '${__galaxy_url__}' >> '${out_log}' 22 && python '${__tool_directory__}/data_manager_refgenie_pull.py' -k "\$API_KEY" -u '${__galaxy_url__}'
23 #if "graceful" in $str($api_refresh):
24 --graceful
25 #end if
26 >> '${out_log}'
23 #end if 27 #end if
24 ]]></command> 28 ]]></command>
25 <inputs> 29 <inputs>
26 <param argument="--assets" name="assets" type="drill_down" display="checkbox" hierarchy="exact" multiple="True" optional="False" label="Select desired asset" dynamic_options="galaxy_code_get_refgenie_assets(__trans__.app.config.refgenie_config_file)" help="string of asset-registry-paths"> 30 <param argument="--assets" name="assets" type="drill_down" display="checkbox" hierarchy="exact" multiple="True" optional="False" label="Select desired asset" dynamic_options="galaxy_code_get_refgenie_assets(__trans__.app.config.refgenie_config_file)" help="string of asset-registry-paths">
27 <validator type="regex" message="You must select an asset, not the remote URL or genome.">.+/.+/.+</validator> 31 <validator type="regex" message="You must select an asset, not the remote URL or genome.">.+/.+/.+</validator>
28 </param> 32 </param>
29 <param argument="--force" name="force" type="boolean" truevalue="--force" falsevalue="" checked="False" label="Force (re-)download" /> 33 <param argument="--force" name="force" type="boolean" truevalue="--force" falsevalue="" checked="False" label="Force (re-)download" />
30 <param argument="--api_refresh" name="api_refresh" type="boolean" truevalue="--api_refresh" falsevalue="" checked="True" label="Refresh Galaxy data tables using API" /> 34 <param name="api_refresh" type="select" label="Refresh Galaxy data tables using API" help="Refresh gracefully will attempt to refresh, but a failure will not be fatal.">
35 <option value="refresh">Refresh</option>
36 <option value="refresh_graceful" selected="True">Refresh gracefully</option>
37 <option value="no">Do not refresh</option>
38 </param>
31 </inputs> 39 </inputs>
32 <outputs> 40 <outputs>
33 <data name="out_file" format="data_manager_json"/> 41 <data name="out_file" format="data_manager_json" label="${tool.name}: data manager json"/>
34 <data name="out_log" format="txt"/> 42 <data name="out_log" format="txt" label="${tool.name}: log file"/>
35 </outputs> 43 </outputs>
36 <tests> 44 <tests>
37 <test> 45 <test>
38 <param name="assets" value="aHR0cDovL3JlZmdlbm9tZXMuZGF0YWJpby5vcmcvdjIvYXNzZXRz/t7/fasta:default"/> 46 <param name="assets" value="aHR0cDovL3JlZmdlbm9tZXMuZGF0YWJpby5vcmcvdjIvYXNzZXRz/t7/fasta:default"/>
39 <param name="force" value="--force"/> 47 <param name="force" value="--force"/>
40 <param name="api_refresh" value=""/> 48 <param name="api_refresh" value="no"/>
41 <output name="out_file"> 49 <output name="out_file">
42 <assert_contents> 50 <assert_contents>
43 <has_text text="{}"/> 51 <has_text text="{}"/>
44 </assert_contents> 52 </assert_contents>
45 </output> 53 </output>
55 63
56 Fetches a reference genome using refgenie (http://refgenie.databio.org). 64 Fetches a reference genome using refgenie (http://refgenie.databio.org).
57 65
58 .. class:: infomark 66 .. class:: infomark
59 67
60 **Notice:** Galaxy data tables will be refreshed using API calls. 68 **Notice:** Galaxy data tables will be refreshed using API calls. You must have configured Galaxy to work with refgenie, see https://galaxyproject.org/admin/refgenie/.
61 69
62 .. class:: warning 70 .. class:: warning
63 71
64 **You must configure Galaxy to use refgenie, by setting 'refgenie_config_file' in the Galaxy config. This tool uses refgenie config file version 0.4.** 72 **You must configure Galaxy to use refgenie, by setting 'refgenie_config_file' in the Galaxy config. This tool uses refgenie config file version 0.4.**
65 ]]></help> 73 ]]></help>