Mercurial > repos > iuc > humann_regroup_table

annotate humann_infer_taxonomy @ 1:c409a495841f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 948cdafe28ae232b641a58bb7dc044d320feb294"
author iuc
date Wed, 19 May 2021 16:57:05 +0000
parents 26ce946f4da9
children
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26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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1 <!-- The tool is broken with current version of HUMAnN. Once it will be fixed, we can update this wrapper and add the XML extension to enable it -->
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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2 <tool id="humann_infer_taxonomy" name="Infex taxonomy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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3 <description>for "unclassified" taxonomy in HUMAnN generated gene families</description>
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4 <macros>
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5 <import>macros.xml</import>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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6 </macros>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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7 <expand macro="edam_ontology"/>
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8 <expand macro="requirements"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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9 <expand macro="version"/>
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10 <command detect_errors="exit_code"><![CDATA[
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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11 humann_infer_taxonomy
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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12 --input '$input'
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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13 --output '$output'
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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14 --level '$level'
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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15 --database '$database.fields.path'
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16 --mode '$mode'
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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17 --lca-choice '$lca_choice'
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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18 --threshold $threshold
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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19 ]]></command>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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20 <inputs>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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21 <param argument="--input" type="data" format="tsv,tabular" label="Gene family table"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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22 <param argument="--level" type="select" label="Desired level for taxonomic estimation/summation">
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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23 <option value="Kingdom">Kingdom</option>
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24 <option value="Phylum">Phylum</option>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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25 <option value="Class">Class</option>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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26 <option value="Order">Order</option>
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27 <option value="Family" selected="true">Family</option>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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28 <option value="Genus">Genus</option>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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29 </param>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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30 <param argument="--database" type="select" label="UniRef-specific taxonomy database">
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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31 <options from_data_table="humann_utility_mapping">
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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32 <validator message="No utility mapping is available" type="no_options" />
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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33 <filter type="regexp" column="2" value="tol-lca" />
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34 </options>
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35 </param>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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36 <param argument="--mode" type="select" label="Rows to include in the estimation/summation">
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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37 <option value="c_tmode" selected="true">Totals</option>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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38 <option value="c_umode">Unclassified</option>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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39 <option value="c_smode">Stratified</option>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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40 </param>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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41 <param argument="--lca-choice" type="select" label="Per-gene taxonomic annotation to consider">
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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42 <option value="source_tax">Source taxonomy</option>
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43 <option value="uniref_lca">UniRef lowest common ancestor (LCA)</option>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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44 <option value="humann_lca" selected="true">HUMAnN lowest common ancestor (LCA)</option>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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45 </param>
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46 <param argument="--threshold" type="float" value="1e-3" label="Minimum frequency for a new taxon to be included"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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47 </inputs>
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48 <outputs>
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49 <data format="tabular" name="output"/>
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50 </outputs>
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51 <tests>
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52 <test expect_num_outputs="1">
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53 <param name="input" value=""/>
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54 <param name="level" value="Kingdom"/>
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55 <param name="database" value=""/>
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56 <param name="mode" value="c_tmode"/>
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57 <param name="lca_choice" value="source_tax"/>
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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58 <param name="threshold" value="1e-3"/>
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59 <output name="output" ftype="tabular">
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60 <assert_contents>
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61 <has_text text=""/>
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62 <has_line line=""/>
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63 <has_line_matching expression=""/>
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64 <has_n_columns n=""/>
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65 <has_size value="" delta=""/>
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66 </assert_contents>
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67 </output>
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68 </test>
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69 </tests>
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70 <help><![CDATA[
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71 @HELP_HEADER@
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72
26ce946f4da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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73 Based on the lowest common ancestor (LCA) annotation
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74 of each UniRef50/90 cluster, this tool infers approximate taxonomy
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75 for unclassified features at a target level of resolution.
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76
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77 It will modify features of known genus/species to match
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78 target level.
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79 ]]></help>
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80 <expand macro="citations"/>
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81 </tool>