Mercurial > repos > nate > data_manager_bowtie2_index_builder

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
author nate
date Tue, 29 Jul 2025 17:13:06 +0000
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6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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2 <description>builder</description>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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3 <macros>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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4 <token name="@WRAPPER_VERSION@">2.5.4</token>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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5 <token name="@VERSION_SUFFIX@">1</token>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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6 </macros>
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7 <requirements>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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8 <requirement type="package" version="@WRAPPER_VERSION@">bowtie2</requirement>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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9 </requirements>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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10 <command detect_errors="exit_code"><![CDATA[
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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11 #set $value = $sequence_id or $all_fasta_source.fields.dbkey
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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12 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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13 mkdir -p '${out_file.extra_files_path}' &&
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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14 ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' &&
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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15 cd '${out_file.extra_files_path}' &&
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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16 bowtie2-build --threads \${GALAXY_SLOTS:-1} '${out_file.extra_files_path}/${fasta_file_name}' '${value}' &&
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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17 rm '${out_file.extra_files_path}/${fasta_file_name}' &&
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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18 cp '$dmjson' '$out_file'
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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19 ]]></command>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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20 <configfiles>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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21 <configfile name="dmjson"><![CDATA[#slurp
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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22 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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23 #set $value = $sequence_id or $all_fasta_source.fields.dbkey
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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24 #set $name = $sequence_name or $all_fasta_source.fields.name
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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25 {
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26 "data_tables":{
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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27 "bowtie2_indexes":[
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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28 {
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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29 "value": "${value}",
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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30 "dbkey": "${all_fasta_source.fields.dbkey}",
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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31 "name": "${name}",
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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32 "path": "${value}"
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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33 }
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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34 #if $tophat2:
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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35 ],
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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36 "tophat2_indexes":[
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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37 {
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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38 "value": "${value}",
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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39 "dbkey": "${all_fasta_source.fields.dbkey}",
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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40 "name": "${name}",
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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41 "path": "${value}"
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42 }
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43 #end if
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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44 ]
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45 }
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46 }
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47 ]]></configfile>
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48 </configfiles>
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49 <inputs>
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50 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
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51 <options from_data_table="all_fasta"/>
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52 </param>
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53 <param name="sequence_name" type="text" value="" label="Name of sequence" />
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54 <param name="sequence_id" type="text" value="" label="ID for sequence" />
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55 <param name="tophat2" type="boolean" checked="True" label="Also make available for TopHat" help="Adds values to tophat2_indexes tool data table" />
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56 </inputs>
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57 <outputs>
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58 <data name="out_file" format="data_manager_json"/>
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59 </outputs>
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60 <tests>
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61 <test>
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62 <param name="all_fasta_source" value="phiX174"/>
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63 <output name="out_file" value="bowtie2_data_manager.1.json"/>
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64 </test>
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65 <test>
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66 <param name="all_fasta_source" value="phiX174"/>
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67 <param name="sequence_name" value="Galeocerdo cuvier"/>
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68 <param name="sequence_id" value="tigHai1"/>
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69 <param name="tophat2" value="False"/>
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70 <output name="out_file" file="bowtie2_data_manager.2.json"/>
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71 </test>
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72 </tests>
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73
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74 <help>
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75 .. class:: infomark
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76
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77 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
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78 </help>
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79 </tool>