Mercurial > repos > iuc > checkm2_build_database

annotate data_manager/checkm2_datamanager.xml @ 0:34dc5b5f35ca draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
author iuc
date Tue, 14 Jan 2025 20:26:31 +0000
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children 757826aa89c3
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34dc5b5f35ca 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@">
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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2 <description>database builder</description>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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3 <macros>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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4 <!-- on update run a local test setting `test` to something else than "true" -->
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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5 <token name="@TOOL_VERSION@">1.0.2</token>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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6 <token name="@VERSION_SUFFIX@">0</token>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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7 <token name="@PROFILE@">23.1</token>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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8 </macros>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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9 <requirements>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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10 <requirement type="package" version="@TOOL_VERSION@">checkm2</requirement>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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11 </requirements>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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12 <version_command>checkm2 --version</version_command>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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13 <command detect_errors="exit_code"><![CDATA[
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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14 mkdir -p '$out_file.extra_files_path' &&
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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15 #if $test != "true"
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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16 checkm2 database --download --path '$out_file.extra_files_path'/ &&
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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17 mv '$out_file.extra_files_path'/CheckM2_database/uniref100.KO.1.dmnd '$out_file.extra_files_path' &&
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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18 #else
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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19 touch '$out_file.extra_files_path'/uniref100.KO.1.dmnd &&
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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20 #end if
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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21 cp '$dmjson' '$out_file'
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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22 ]]></command>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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23 <configfiles>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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24 <configfile name="dmjson"><![CDATA[
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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25 {
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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26 "data_tables":{
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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27 "checkm2":[
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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28 {
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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29 "path":"uniref100.KO.1.dmnd",
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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30 "name":"CheckM2 diamond DB downloaded with version @TOOL_VERSION@",
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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31 "version":"@TOOL_VERSION@",
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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32 "value":"@TOOL_VERSION@"
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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33 }
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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34 ]
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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35 }
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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36 }]]>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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37 </configfile>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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38 </configfiles>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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39 <inputs>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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40 <param name="test" type="hidden"/>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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41 </inputs>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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42 <outputs>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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43 <data name="out_file" format="data_manager_json" />
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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44 </outputs>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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45 <tests>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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46 <test expect_num_outputs="1">
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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47 <param name="test" value="true"/>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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48 <output name="out_file">
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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49 <assert_contents>
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50 <has_text text='"value":"@TOOL_VERSION@"'/>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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51 <has_text text='"name":"CheckM2 diamond DB downloaded with version @TOOL_VERSION@"'/>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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52 </assert_contents>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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53 </output>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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54 </test>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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55 </tests>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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56 <help><![CDATA[
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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57 Download and extract CheckM2 reference data.
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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58 ]]></help>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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59 <citations>
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60 <citation type="doi">10.1038/s41592-023-01940-w</citation>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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61 </citations>
34dc5b5f35ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
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62 </tool>