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 5d2e5fddec81
children
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5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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1 <tool id="homer_genome_preparse_data_manager" name="Homer genome preparse" tool_type="manage_data" version="@IDX_VERSION@" profile="20.05">
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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2 <requirements>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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3 <requirement type="package" version="@IDX_VERSION@">homer</requirement>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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4 <requirement type="package" version="3.9">python</requirement>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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5 </requirements>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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6 <macros>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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7 <token name="@IDX_VERSION@">4.11</token>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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8 </macros>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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9 <command detect_errors="exit_code"><![CDATA[
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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10 python '$__tool_directory__/homer_genome_preparse.py'
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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11 '${out_file}'
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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12 --fasta_filename '${all_fasta_source.fields.path}'
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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13 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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14 --fasta_description '${all_fasta_source.fields.name}'
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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15 ${mask}
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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16 --size '${size}'
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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17 --index_version '@IDX_VERSION@'
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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18 --data_table_name homer_preparse
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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19 ]]></command>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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20 <inputs>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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21 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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22 <options from_data_table="all_fasta"/>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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23 </param>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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24 <param name="sequence_name" type="text" value="" label="Name of sequence" />
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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25 <param name="sequence_id" type="text" value="" label="ID for sequence" />
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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26 <param name="mask" type="boolean" truevalue="--mask" falsevalue="" checked="False" label="mask repeats/lower case sequence" />
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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27 <param name="size" type="integer" value="200" min="0" label="fragment size to use for motif finding" />
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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28 </inputs>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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29 <outputs>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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30 <data name="out_file" format="data_manager_json"/>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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31 </outputs>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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32 <tests>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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33 <test>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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34 <param name="all_fasta_source" value="phiX174"/>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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35 <output name="out_file" >
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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36 <assert_contents>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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37 <has_text text="{&quot;data_tables&quot;: {&quot;homer_preparse&quot;: [{&quot;dbkey&quot;: &quot;phiX174&quot;, &quot;mask&quot;: &quot;False&quot;, &quot;name&quot;: &quot;phiX174 (200bp)&quot;, &quot;path&quot;: &quot;phiX174_200&quot;, &quot;path_fasta&quot;:" />
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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38 <has_text text="test-data/phiX174.fasta&quot;, &quot;size&quot;: &quot;200&quot;, &quot;value&quot;: &quot;phiX174_200&quot;, &quot;version&quot;: &quot;4.11&quot;}]}}" />
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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39 </assert_contents>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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40 </output>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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41 </test>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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42 <test>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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43 <param name="all_fasta_source" value="phiX174"/>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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44 <param name="mask" value="True"/>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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45 <param name="size" value="100"/>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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46 <output name="out_file" >
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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47 <assert_contents>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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48 <has_text text="{&quot;data_tables&quot;: {&quot;homer_preparse&quot;: [{&quot;dbkey&quot;: &quot;phiX174&quot;, &quot;mask&quot;: &quot;True&quot;, &quot;name&quot;: &quot;phiX174 masked (100bp)&quot;, &quot;path&quot;: &quot;phiX174r_100&quot;, &quot;path_fasta&quot;:" />
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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49 <has_text text="test-data/phiX174.fasta&quot;, &quot;size&quot;: &quot;100&quot;, &quot;value&quot;: &quot;phiX174r_100&quot;, &quot;version&quot;: &quot;4.11&quot;}]}}" />
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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50 </assert_contents>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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51 </output>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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52 </test>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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53 </tests>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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54
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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55 <help>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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56 .. class:: infomark
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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57
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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58 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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59 </help>
5d2e5fddec81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
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60 </tool>