Mercurial > repos > iuc > data_manager_bowtie_index_builder

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
author iuc
date Thu, 05 Dec 2024 06:47:05 +0000
parents a230fefc187a
children
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a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
iuc
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1 <tool id="bowtie_index_builder_data_manager" name="Bowtie index" tool_type="manage_data" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
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2 <description>builder</description>
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a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
iuc
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3 <macros>
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
iuc
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4 <token name="@WRAPPER_VERSION@">1.3.1</token>
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
iuc
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5 <token name="@VERSION_SUFFIX@">0</token>
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@WRAPPER_VERSION@">bowtie</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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11 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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12 mkdir -p '${out_file.extra_files_path}' &&
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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13 ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' &&
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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14 bowtie-build '${out_file.extra_files_path}/${fasta_file_name}' '${out_file.extra_files_path}/${fasta_file_name}' &&
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
iuc
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15 cp '$dmjson' '$out_file'
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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16 ]]>
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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17 </command>
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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18 <configfiles>
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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19 <configfile name="dmjson"><![CDATA[#slurp
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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20 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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21 #set $value = $sequence_id or $all_fasta_source.fields.dbkey
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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22 #set $name = $sequence_name or $all_fasta_source.fields.name
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
iuc
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23 {
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24 "data_tables":{
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
iuc
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25 "bowtie_indexes":[
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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26 {
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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27 "value": "${value}",
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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28 "dbkey": "${all_fasta_source.fields.dbkey}",
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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29 "name": "${name}",
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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30 "path": "${fasta_file_name}"
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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31 }
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32 ]
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33 }
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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34 }
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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35 ]]></configfile>
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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36 </configfiles>
0
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37 <inputs>
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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38 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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39 <options from_data_table="all_fasta"/>
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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40 </param>
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41 <param name="sequence_name" type="text" value="" label="Name of sequence" help="Leave blank to use all_fasta name" />
a230fefc187a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
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42 <param name="sequence_id" type="text" value="" label="ID for sequence" help="Leave blank to use all_fasta id" />
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ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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43 </inputs>
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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44 <outputs>
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45 <data name="out_file" format="data_manager_json"/>
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46 </outputs>
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47 <tests>
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48 <test>
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49 <param name="all_fasta_source" value="phiX174"/>
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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50 <output name="out_file" file="bowtie_data_manager.1.json"/>
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51 </test>
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52 <test>
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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53 <param name="all_fasta_source" value="phiX174"/>
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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54 <param name="sequence_name" value="Galeocerdo cuvier"/>
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55 <param name="sequence_id" value="tigHai1"/>
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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56 <output name="out_file" file="bowtie_data_manager.2.json"/>
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57 </test>
a601bb53be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
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58 </tests>
4
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59 <help><![CDATA[
0
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60 .. class:: infomark
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61
4
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62 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
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63 ]]></help>
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64 <citations>
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65 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
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66 </citations>
0
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67 </tool>