Mercurial > repos > iuc > checkm2_build_database
annotate data_manager/checkm2_datamanager.xml @ 1:64630d815957 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit 043f6bb449b27287b413a937b21d918569cfdad7
author | iuc |
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date | Sun, 19 Jan 2025 18:48:14 +0000 |
parents | 4abc306ec842 |
children | df2f47a0e57a |
rev | line source |
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0
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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1 <tool id="checkm2_build_database" name="CheckM2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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2 <description>database builder</description> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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3 <macros> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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4 <!-- on update run a local test setting `test` to something else than "true" --> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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5 <token name="@TOOL_VERSION@">1.0.2</token> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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6 <token name="@VERSION_SUFFIX@">0</token> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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7 <token name="@PROFILE@">23.1</token> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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8 </macros> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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9 <requirements> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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10 <requirement type="package" version="@TOOL_VERSION@">checkm2</requirement> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
parents:
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11 </requirements> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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12 <version_command>checkm2 --version</version_command> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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13 <command detect_errors="exit_code"><![CDATA[ |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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14 mkdir -p '$out_file.extra_files_path' && |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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15 #if $test != "true" |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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16 checkm2 database --download --path '$out_file.extra_files_path'/ && |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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17 mv '$out_file.extra_files_path'/CheckM2_database/uniref100.KO.1.dmnd '$out_file.extra_files_path' && |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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18 #else |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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19 touch '$out_file.extra_files_path'/uniref100.KO.1.dmnd && |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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20 #end if |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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21 cp '$dmjson' '$out_file' |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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22 ]]></command> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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23 <configfiles> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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24 <configfile name="dmjson"><![CDATA[ |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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25 { |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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26 "data_tables":{ |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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27 "checkm2":[ |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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28 { |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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29 "path":"uniref100.KO.1.dmnd", |
1
64630d815957
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit 043f6bb449b27287b413a937b21d918569cfdad7
iuc
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30 "dbkey":"@TOOL_VERSION@", |
0
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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31 "name":"CheckM2 diamond DB downloaded with version @TOOL_VERSION@", |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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32 "version":"@TOOL_VERSION@", |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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33 "value":"@TOOL_VERSION@" |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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34 } |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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35 ] |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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36 } |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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37 }]]> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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38 </configfile> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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39 </configfiles> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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40 <inputs> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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41 <param name="test" type="hidden"/> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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42 </inputs> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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43 <outputs> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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44 <data name="out_file" format="data_manager_json" /> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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45 </outputs> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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46 <tests> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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47 <test expect_num_outputs="1"> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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48 <param name="test" value="true"/> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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49 <output name="out_file"> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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50 <assert_contents> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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51 <has_text text='"value":"@TOOL_VERSION@"'/> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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52 <has_text text='"name":"CheckM2 diamond DB downloaded with version @TOOL_VERSION@"'/> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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53 </assert_contents> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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54 </output> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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55 </test> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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56 </tests> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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57 <help><![CDATA[ |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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58 Download and extract CheckM2 reference data. |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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59 ]]></help> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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60 <citations> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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61 <citation type="doi">10.1038/s41592-023-01940-w</citation> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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62 </citations> |
4abc306ec842
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
iuc
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63 </tool> |