Mercurial > repos > iuc > data_manager_homer_preparse

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
author iuc
date Sun, 16 Apr 2023 08:27:25 +0000
parents 20fae63ba8dc
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20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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1 <tool id="homer_install_promoters_data_manager" name="Homer install promoter DB" tool_type="manage_data" version="@TOOL_VERSION@" profile="22.01">
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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2 <requirements>
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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3 <requirement type="package" version="@TOOL_VERSION@">homer</requirement>
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4 <requirement type="package" version="3.11">python</requirement>
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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5 </requirements>
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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6 <macros>
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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7 <token name="@TOOL_VERSION@">4.11</token>
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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8 </macros>
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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9 <command detect_errors="exit_code"><![CDATA[
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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10 cp -r \$(dirname \$(which findMotifs.pl))/../share/homer ./ &&
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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11 perl ./homer/configureHomer.pl -install ${organism}-p ${organism}-o -keepScript &&
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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13 organism_version=\$(cat homer/config.txt | grep "accession and ontology information" | grep $organism | cut -f 2) &&
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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14 promoter_version=\$(cat homer/config.txt | grep promoters | grep $organism | cut -f 2) &&
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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15
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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16 python '$__tool_directory__/homer_install_promoters.py'
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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17 '${out_file}'
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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18 --organism $organism
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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19 --organism_version \${organism_version}
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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20 --promoter_version \${promoter_version}
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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21 --data_table_name homer_promoters
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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22 --DB_path homer
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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23 ]]></command>
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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24 <inputs>
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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25 <param name="organism" type="select" label="Select a target organism to download" help="Promoter, GO and accession information will be downloaded and the data dir will be stored to reduce the network bandwidth during execution of the tool. Always the newest available version will be downloaded.">
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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26 <option value="arabidopsis">arabidopsis (Arabidopsis thaliana)</option>
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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27 <option value="chicken">chicken (Gallus gallus)</option>
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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28 <option value="fly">fly (Drosophila melanogaster)</option>
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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29 <option value="frog">frog (Xenopus tropicalis)</option>
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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30 <option value="human">human (Homo sapiens)</option>
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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31 <option value="mouse">mouse (Mus musculus)</option>
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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32 <option value="rat">rat (Rattus norvegicus)</option>
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33 <option value="worm" selected="true">worm (Caenorhabditis elegans)</option>
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34 <option value="yeast">yeast (Saccharomyces cerevisiae)</option>
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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35 <option value="zebrafish">zebrafish (Danio rerio)</option>
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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36 </param>
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37 </inputs>
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38 <outputs>
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39 <data name="out_file" format="data_manager_json"/>
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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40 </outputs>
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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41 <tests>
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42 <test>
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43 <param name="organism" value="worm"/>
20fae63ba8dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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44 <output name="out_file">
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45 <assert_contents>
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46 <has_text text="{&quot;data_tables&quot;: {&quot;homer_promoters&quot;: [{&quot;dbkey&quot;: &quot;worm_"/>
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47 <has_text text="&quot;organism_version&quot;: &quot;v"/>
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48 <has_text text="&quot;promoter_version&quot;: &quot;v"/>
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49 <has_text text="&quot;organism&quot;: &quot;worm&quot;"/>
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50 <has_text text="&quot;path&quot;: &quot;"/>
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51 </assert_contents>
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52 </output>
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53 </test>
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54 </tests>
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55 <help>
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56 </help>
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57 </tool>