Mercurial > repos > blankenberglab > data_manager_refgenie_pull

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