Mercurial > repos > iuc > extract_metaphlan_database

annotate extract_metaphlan_database.xml @ 10:39180ac12d65 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan commit 26cbf16569d13b7ddbbbd99fc49ec15ce312a992
author iuc
date Fri, 14 Nov 2025 13:46:43 +0000
parents b81c6e597cf1
children
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1 <tool id="extract_metaphlan_database" name="Extract the marker sequences and metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>from the MetaPhlAn database</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="edam_ontology"/>
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7 <expand macro="requirements"/>
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8 <version_command>metaphlan -v</version_command>
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9 <command detect_errors="aggressive"><![CDATA[
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10 bowtie2-inspect
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11 '${cached_db.fields.path}/${cached_db.fields.dbkey}'
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12 > '$sequences'
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14 &&
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16 python '$__tool_directory__/customizemetadata.py'
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17 transform_pkl_to_json
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18 --pkl '${cached_db.fields.path}/${cached_db.fields.dbkey}.pkl'
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19 --json '$metadata'
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20 ]]></command>
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21 <inputs>
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22 <param name="cached_db" label="Cached database with clade-specific marker genes" type="select">
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23 <options from_data_table="@IDX_DATA_TABLE@">
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24 <filter type="static_value" column="4" value="@IDX_VERSION@"/>
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25 <validator message="No MetaPhlAn database is available" type="no_options"/>
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26 </options>
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27 </param>
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28 </inputs>
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29 <outputs>
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30 <data name="sequences" format="fasta" label="${tool.name} on ${on_string}: Marker seqeunces from MetaPhlAn database"/>
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31 <data name="metadata" format="json" label="${tool.name} on ${on_string}: Marker metadata from MetaPhlAn database"/>
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32 </outputs>
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33 <tests>
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34 <test expect_num_outputs="2">
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35 <param name="cached_db" value="test-db-20210409"/>
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36 <output name="sequences" file="test-db.fasta" ftype="fasta" compare="sim_size">
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37 <assert_contents>
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38 <has_line line=">13076__A0A2I1PE66__CYJ72_10760 UniRef90_A0A2I1PE66;k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella|s__Globicatella_sanguinis;GCA_002847845"/>
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39 </assert_contents>
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40 </output>
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41 <output name="metadata" file="test-db.json" ftype="json" compare="sim_size">
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42 <assert_contents>
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43 <has_text text="13076__A0A2I1PE66__CYJ72_10760"/>
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44 <has_text text="k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella|s__Globicatella_sanguinis"/>
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45 <has_text text="GCA_002847845"/>
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46 <has_text text="clade"/>
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47 <has_text text="ext"/>
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48 <has_text text="len"/>
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49 <has_text text="taxon"/>
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50 <has_text text="markers"/>
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51 <has_text text="taxonomy"/>
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52 <has_text text="merged_taxon"/>
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53 </assert_contents>
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54 </output>
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55 </test>
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56 </tests>
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57 <help><![CDATA[
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58 What it does
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59 ============
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60
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61 Reconstruct the marker sequences (in fasta format) and metadata (in JSON) from the MetaPhlAn BowTie2 database
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62
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63 Outputs
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64 =======
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65
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66 - Fasta file with marker sequences.
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67
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68 This file can be used to add new marker sequences and then customizing the database.
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69
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70 - JSON file with marker metadata
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71
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72 ]]></help>
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73 <expand macro="citations"/>
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74 </tool>