Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_fragment-insertion_classify-otus-experimental.xml @ 0:370e0b6e9826 draft
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| author | florianbegusch |
|---|---|
| date | Wed, 17 Jul 2019 03:05:17 -0400 |
| parents | |
| children | f190567fe3f6 |
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| -1:000000000000 | 0:370e0b6e9826 |
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| 1 <?xml version="1.0" ?> | |
| 2 <tool id="qiime_fragment-insertion_classify-otus-experimental" name="qiime fragment-insertion classify-otus-experimental" version="2019.4"> | |
| 3 <description> - Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2019.4">qiime2</requirement> | |
| 6 </requirements> | |
| 7 <command><![CDATA[ | |
| 8 qiime fragment-insertion classify-otus-experimental | |
| 9 | |
| 10 --i-representative-sequences=$irepresentativesequences | |
| 11 --i-tree=$itree --o-classification=oclassification | |
| 12 | |
| 13 | |
| 14 #if str( $id_to_taxonomy_fp.selector ) == 'history' | |
| 15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp | |
| 16 --i-reference-taxonomy '$tax' | |
| 17 #else: | |
| 18 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path | |
| 19 --i-reference-taxonomy '$tax' | |
| 20 #end if | |
| 21 | |
| 22 | |
| 23 ; | |
| 24 cp oclassification.qza $oclassification | |
| 25 ]]></command> | |
| 26 <inputs> | |
| 27 <param format="qza,no_unzip.zip" label="--i-representative-sequences: ARTIFACT FeatureData[Sequence] The sequences used for a 'sepp' run to produce the 'tree'. [required]" name="irepresentativesequences" optional="False" type="data"/> | |
| 28 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT The tree resulting from inserting fragments into a Phylogeny[Rooted] reference phylogeny, i.e. the output of function 'sepp' [required]" name="itree" optional="False" type="data"/> | |
| 29 | |
| 30 <conditional name="id_to_taxonomy_fp" optional="True"> | |
| 31 <param name="selector" type="select" label="Reference taxonomy to query"> | |
| 32 <option value="cached">Public databases</option> | |
| 33 <option value="history">Databases from your history</option> | |
| 34 </param> | |
| 35 <when value="cached"> | |
| 36 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True"> | |
| 37 <options from_data_table="qiime_taxonomy" /> | |
| 38 </param> | |
| 39 </when> | |
| 40 <when value="history"> | |
| 41 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" /> | |
| 42 </when> | |
| 43 </conditional> | |
| 44 | |
| 45 </inputs> | |
| 46 <outputs> | |
| 47 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/> | |
| 48 </outputs> | |
| 49 <help><![CDATA[ | |
| 50 Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny. | |
| 51 ####################################################################################### | |
| 52 | |
| 53 Experimental: Use the resulting tree from 'sepp' and find closest OTU-ID | |
| 54 for every inserted fragment. Then, look up the reference lineage string in | |
| 55 the reference taxonomy. | |
| 56 | |
| 57 Parameters | |
| 58 ---------- | |
| 59 representative_sequences : FeatureData[Sequence] | |
| 60 The sequences used for a 'sepp' run to produce the 'tree'. | |
| 61 tree : Phylogeny[Rooted] | |
| 62 The tree resulting from inserting fragments into a reference phylogeny, | |
| 63 i.e. the output of function 'sepp' | |
| 64 reference_taxonomy : FeatureData[Taxonomy], optional | |
| 65 Reference taxonomic table that maps every OTU-ID into a taxonomic | |
| 66 lineage string. | |
| 67 | |
| 68 Returns | |
| 69 ------- | |
| 70 classification : FeatureData[Taxonomy] | |
| 71 Taxonomic lineages for inserted fragments. | |
| 72 ]]></help> | |
| 73 <macros> | |
| 74 <import>qiime_citation.xml</import> | |
| 75 </macros> | |
| 76 <expand macro="qiime_citation"/> | |
| 77 </tool> |