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 08:30:23 +0000
parents d9c177013aba
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d9c177013aba 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">
d9c177013aba 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>
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3 <requirement type="package" version="@TOOL_VERSION@">homer</requirement>
d9c177013aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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4 <requirement type="package" version="3.11">python</requirement>
d9c177013aba 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>
d9c177013aba 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>
d9c177013aba 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>
d9c177013aba 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>
d9c177013aba 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[
d9c177013aba 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 ./ &&
d9c177013aba 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 &&
d9c177013aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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d9c177013aba 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) &&
d9c177013aba 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 $organism | cut -f 2) &&
d9c177013aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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d9c177013aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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16 python '$__tool_directory__/homer_install_promoters.py'
d9c177013aba 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}'
d9c177013aba 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
d9c177013aba 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}
d9c177013aba 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}
d9c177013aba 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
d9c177013aba 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
d9c177013aba 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>
d9c177013aba 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>
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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.">
d9c177013aba 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>
d9c177013aba 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>
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28 <option value="fly">fly (Drosophila melanogaster)</option>
d9c177013aba 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>
d9c177013aba 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>
d9c177013aba 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>
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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>
d9c177013aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 16a919905f336e34e237388c1921d0f4f8a368af
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34 <option value="yeast">yeast (Saccharomyces cerevisiae)</option>
d9c177013aba 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>
d9c177013aba 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"/>
d9c177013aba 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>
d9c177013aba 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"/>
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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>