Mercurial > repos > iuc > data_manager_build_kma_index

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1
author iuc
date Fri, 10 Oct 2025 12:03:01 +0000
parents eb620aa70b61
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eb620aa70b61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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1 <?xml version="1.0"?>
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2 <tool id="kma_build_index" name="KMA Index Builder" tool_type="manage_data" version="1.6.6+galaxy0" profile="24.1">
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3 <description>kma index builder</description>
eb620aa70b61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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4 <requirements>
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5 <requirement type="package" version="1.6.6">kma</requirement>
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6 </requirements>
eb620aa70b61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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7 <version_command>kma -v</version_command>
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8 <command detect_errors="exit_code">
eb620aa70b61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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9 <![CDATA[
3
def26737cedb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1
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10 mkdir -p '${out_file.extra_files_path}'/index_folder &&
def26737cedb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1
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11 kma_index
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12 -i '$fasta'
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13 -o '${out_file.extra_files_path}'/index_folder/index
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14 ## index options
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15 -k $k
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16 -k_t $k_t
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17 -k_i $k_i
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18 -ML $ML
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19 -ht $ht
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20 -hq $hq
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21 ]]></command>
def26737cedb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1
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22 <configfiles>
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23 <configfile filename="dm.json"><![CDATA[#slurp
def26737cedb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1
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24 #from datetime import datetime
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25 #from hashlib import md5
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26 #set value=datetime.now().strftime("%Y-%m-%d") + "_" + md5($name.encode()).hexdigest()
def26737cedb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1
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27 {"data_tables": {"kma_index": [{"value": "$value", "name": "$name", "path": "index_folder"}]}}
def26737cedb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1
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28 ]]></configfile>
def26737cedb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1
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29 </configfiles>
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30 <inputs>
3
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31 <param argument="-k" type="integer" value="16" min="8" max="32" label="kmer size used for indexing the database." />
def26737cedb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1
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32 <param argument="-k_t" type="integer" value="16" min="8" max="32" label="kmer size used to identify template candidates when running KMA." />
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33 <param argument="-k_i" type="integer" value="16" min="8" max="32" label="kmer size used when performing alignments between two sequences." />
def26737cedb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1
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34 <param argument="-ML" type="integer" value="16" label="Minimum length of templates" />
def26737cedb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1
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35 <param argument="-ht" type="float" value="1.0" min="0.0" max="1.0" label="Homology template" />
def26737cedb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1
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36 <param argument="-hq" type="float" value="1.0" min="0.0" max="1.0" label="Homology query" />
def26737cedb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1
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37 <param name="fasta" type="data" format="fasta" label="Sequence to index (fasta)" />
def26737cedb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1
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38 <param name="name" type="text" optional="false" label="Name for index" help="Choose a name that describes the indexed sequence and possibly any non-default indexing parameters.">
def26737cedb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1
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39 <validator type="empty_field"/>
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40 </param>
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41 </inputs>
eb620aa70b61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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42 <outputs>
3
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43 <data name="out_file" format="data_manager_json" from_work_dir="dm.json"/>
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="fasta" value="phiX174.fasta"/>
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48 <param name="name" value="index"/>
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49 <output name="out_file" ftype="data_manager_json">
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50 <assert_contents>
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51 <has_text text='"kma_index":' />
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52 <has_text text='"name": "index"' />
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53 <has_text text='"path": "index_folder"' />
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54 <has_text_matching expression='"value": "\d{4}-\d{2}-\d{2}_6a992d5529f459a44fee58c733255e86"' />
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55 </assert_contents>
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56 </output>
0
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57 </test>
eb620aa70b61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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58 </tests>
3
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59 <help><![CDATA[
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60 **Data manager for building an index for the kma aligner**
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61
def26737cedb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1
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62 Runs the kma index command on the input sequence with the chosen options.
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63
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64 .. class:: infomark
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65
def26737cedb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1
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66 You may want to capture details about the reference sequence and any non-default indexing parameters in the name of the index so that users have a better idea what they are selecting for tool runs.
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67 ]]></help>
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68 <citations>
eb620aa70b61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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69 <citation type="doi">10.1186/s12859-018-2336-6</citation>
eb620aa70b61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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70 </citations>
eb620aa70b61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
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71 </tool>