Mercurial > repos > nate > 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 5c5d8acf6955dc4f404998ac7929f13363ef2c41
author nate
date Tue, 29 Jul 2025 17:12:20 +0000
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eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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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">
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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2 <description>builder</description>
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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3 <macros>
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4 <token name="@WRAPPER_VERSION@">1.3.1</token>
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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5 <token name="@VERSION_SUFFIX@">1</token>
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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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>
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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9 </requirements>
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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10 <command detect_errors="exit_code"><![CDATA[
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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11 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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12 mkdir -p '${out_file.extra_files_path}' &&
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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13 ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' &&
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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14 bowtie-build '${out_file.extra_files_path}/${fasta_file_name}' '${out_file.extra_files_path}/${fasta_file_name}' &&
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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15 rm '${out_file.extra_files_path}/${fasta_file_name}' &&
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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16 cp '$dmjson' '$out_file'
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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17 ]]>
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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18 </command>
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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19 <configfiles>
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20 <configfile name="dmjson"><![CDATA[#slurp
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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21 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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22 #set $value = $sequence_id or $all_fasta_source.fields.dbkey
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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23 #set $name = $sequence_name or $all_fasta_source.fields.name
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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24 {
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25 "data_tables":{
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26 "bowtie_indexes":[
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27 {
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28 "value": "${value}",
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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29 "dbkey": "${all_fasta_source.fields.dbkey}",
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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30 "name": "${name}",
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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31 "path": "${fasta_file_name}"
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32 }
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33 ]
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34 }
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35 }
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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36 ]]></configfile>
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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37 </configfiles>
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38 <inputs>
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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39 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
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40 <options from_data_table="all_fasta"/>
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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41 </param>
eef68fde2b29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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42 <param name="sequence_name" type="text" value="" label="Name of sequence" help="Leave blank to use all_fasta name" />
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43 <param name="sequence_id" type="text" value="" label="ID for sequence" help="Leave blank to use all_fasta id" />
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44 </inputs>
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45 <outputs>
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46 <data name="out_file" format="data_manager_json"/>
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="all_fasta_source" value="phiX174"/>
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51 <output name="out_file" file="bowtie_data_manager.1.json"/>
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52 </test>
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53 <test>
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54 <param name="all_fasta_source" value="phiX174"/>
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55 <param name="sequence_name" value="Galeocerdo cuvier"/>
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56 <param name="sequence_id" value="tigHai1"/>
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57 <output name="out_file" file="bowtie_data_manager.2.json"/>
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58 </test>
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59 </tests>
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60 <help><![CDATA[
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61 .. class:: infomark
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62
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63 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
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64 ]]></help>
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65 <citations>
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66 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
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67 </citations>
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68 </tool>