Mercurial > repos > iuc > extract_metaphlan_database

annotate extract_metaphlan_database.xml @ 4:97ad0d817a45 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2cec4cbdc43f84720af3e22eb008e9788481ce00"
author iuc
date Wed, 02 Feb 2022 22:02:12 +0000
parents 5b2f8b6a3609
children 5eccd3d336a3
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5b2f8b6a3609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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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 > '$sequences'
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13
5b2f8b6a3609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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14 &&
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15
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16 python '$__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 '$metadata'
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20 ]]></command>
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21 <inputs>
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22 <param name="cached_db" label="Cached database with clade-specific marker genes" type="select">
5b2f8b6a3609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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23 <options from_data_table="metaphlan_database">
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24 <validator message="No MetaPhlAn database is available" type="no_options" />
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25 </options>
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26 </param>
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27 </inputs>
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28 <outputs>
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29 <data name="sequences" format="fasta" label="${tool.name} on ${on_string}: Marker seqeunces from MetaPhlAn database" />
5b2f8b6a3609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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30 <data name="metadata" format="json" label="${tool.name} on ${on_string}: Marker metadata from MetaPhlAn database" />
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31 </outputs>
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32 <tests>
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33 <test expect_num_outputs="2">
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34 <param name="cached_db" value="test-db-20210409"/>
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35 <output name="sequences" file="test-db.fasta" ftype="fasta" compare="sim_size">
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36 <assert_contents>
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37 <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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38 </assert_contents>
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39 </output>
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40 <output name="metadata" file="test-db.json" ftype="json" compare="sim_size">
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41 <assert_contents>
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42 <has_text text="13076__A0A2I1PE66__CYJ72_10760"/>
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43 <has_text text="k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella|s__Globicatella_sanguinis"/>
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44 <has_text text="GCA_002847845"/>
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45 <has_text text="clade"/>
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46 <has_text text="ext"/>
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47 <has_text text="len"/>
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48 <has_text text="taxon"/>
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49 <has_text text="markers"/>
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50 <has_text text="taxonomy"/>
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51 <has_text text="merged_taxon"/>
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52 </assert_contents>
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53 </output>
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54 </test>
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55 </tests>
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56 <help><![CDATA[
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57 What it does
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58 ============
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59
5b2f8b6a3609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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60 Reconstruct the marker sequences (in fasta format) and metadata (in JSON) from the MetaPhlAn BowTie2 database
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61
5b2f8b6a3609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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62 Outputs
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63 =======
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64
5b2f8b6a3609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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65 - Fasta file with marker sequences.
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66
5b2f8b6a3609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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67 This file can be used to add new marker sequences and then customizing the database.
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68
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69 - JSON file with marker metadata
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70
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71 ]]></help>
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72 <expand macro="citations"/>
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73 </tool>