Mercurial > repos > blankenberglab > data_manager_refgenie_pull

annotate data_manager/data_manager_refgenie_pull.xml @ 5:0445344b7c3f 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 16:02:32 +0000
parents f80b9af92d97
children
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0445344b7c3f "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
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1 <tool id="data_manager_refgenie_pull" name="refgenie asset pulling" version="@VERSION@+galaxy0" tool_type="manage_data" profile="20.05">
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659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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2 <description>from remote resource</description>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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3 <macros>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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4 <import>macros.xml</import>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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5 </macros>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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6 <requirements>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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7 <requirement type="package" version="@VERSION@">refgenie</requirement>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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8 </requirements>
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f80b9af92d97 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 9a36112c745f111e68a29cee063e0b36448eb303"
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9 <version_command>refgenie --version</version_command>
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659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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10 <code file="data_manager_refgenie_pull.py" />
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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11 <environment_variables>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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12 <environment_variable name="API_KEY" inject="api_key" />
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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13 </environment_variables>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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14 <command detect_errors="exit_code"><![CDATA[
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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15 #for $asset in $assets:
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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16 #set ga = str($asset).split('/',2)
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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17 refgenie pull -c '$__app__.config.refgenie_config_file' -g '$ga[1]' '$ga[2]' $force >> '${out_log}' 2>&1
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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18 &&
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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19 #end for
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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20 echo '{}' > '${out_file}'
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0445344b7c3f "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
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21 #if "refresh" in $str($api_refresh):
0445344b7c3f "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
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22 && python '${__tool_directory__}/data_manager_refgenie_pull.py' -k "\$API_KEY" -u '${__galaxy_url__}'
0445344b7c3f "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
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23 #if "graceful" in $str($api_refresh):
0445344b7c3f "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
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24 --graceful
0445344b7c3f "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
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25 #end if
0445344b7c3f "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
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26 >> '${out_log}'
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659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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27 #end if
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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28 ]]></command>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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29 <inputs>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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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">
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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31 <validator type="regex" message="You must select an asset, not the remote URL or genome.">.+/.+/.+</validator>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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32 </param>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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33 <param argument="--force" name="force" type="boolean" truevalue="--force" falsevalue="" checked="False" label="Force (re-)download" />
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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.">
0445344b7c3f "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
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35 <option value="refresh">Refresh</option>
0445344b7c3f "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
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36 <option value="refresh_graceful" selected="True">Refresh gracefully</option>
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37 <option value="no">Do not refresh</option>
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38 </param>
0
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39 </inputs>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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40 <outputs>
5
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41 <data name="out_file" format="data_manager_json" label="${tool.name}: data manager json"/>
0445344b7c3f "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
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42 <data name="out_log" format="txt" label="${tool.name}: log file"/>
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43 </outputs>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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44 <tests>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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45 <test>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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46 <param name="assets" value="aHR0cDovL3JlZmdlbm9tZXMuZGF0YWJpby5vcmcvdjIvYXNzZXRz/t7/fasta:default"/>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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47 <param name="force" value="--force"/>
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48 <param name="api_refresh" value="no"/>
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49 <output name="out_file">
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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50 <assert_contents>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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51 <has_text text="{}"/>
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52 </assert_contents>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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53 </output>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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54 <output name="out_log">
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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55 <assert_contents>
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56 <has_text text="Download complete"/>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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57 </assert_contents>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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58 </output>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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59 </test>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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60 </tests>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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61 <help><![CDATA[
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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62 **What it does**
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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63
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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64 Fetches a reference genome using refgenie (http://refgenie.databio.org).
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65
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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66 .. class:: infomark
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67
5
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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/.
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69
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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70 .. class:: warning
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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71
2
f5401ae34455 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit b1d0969e9fb5605e259d568c38400bf143b19d2a"
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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.**
0
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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73 ]]></help>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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74 <citations>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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75 <citation type="doi">10.1093/gigascience/giz149</citation>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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76 <citation type="doi">10.1101/2020.10.09.327114</citation>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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77 </citations>
659bfadcd8c6 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit 8d3537d4a138f34f831a629d6be37e3ee6581bc2"
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78 </tool>