Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2-2020.8/qiime_fragment-insertion_classify-otus-experimental.xml @ 20:d93d8888f0b0 draft
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| author | florianbegusch |
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| date | Fri, 04 Sep 2020 12:44:24 +0000 |
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| 19:6c48f8d82424 | 20:d93d8888f0b0 |
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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" | |
| 3 version="2020.8"> | |
| 4 <description>Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.</description> | |
| 5 <requirements> | |
| 6 <requirement type="package" version="2020.8">qiime2</requirement> | |
| 7 </requirements> | |
| 8 <command><![CDATA[ | |
| 9 qiime fragment-insertion classify-otus-experimental | |
| 10 | |
| 11 --i-representative-sequences=$irepresentativesequences | |
| 12 | |
| 13 --i-tree=$itree | |
| 14 | |
| 15 --i-reference-taxonomy=$ireferencetaxonomy | |
| 16 | |
| 17 --o-classification=oclassification | |
| 18 | |
| 19 #if str($examples) != 'None': | |
| 20 --examples=$examples | |
| 21 #end if | |
| 22 | |
| 23 ; | |
| 24 cp oclassification.qza $oclassification | |
| 25 | |
| 26 ]]></command> | |
| 27 <inputs> | |
| 28 <param format="qza,no_unzip.zip" label="--i-representative-sequences: ARTIFACT FeatureData[Sequence] The sequences used for a \'sepp\' run to produce the \'tree\'. [required]" name="irepresentativesequences" optional="False" type="data" /> | |
| 29 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT The tree resulting from inserting fragments into a Phylogeny[Rooted] reference phylogeny, i.e. the output of function \'sepp\' [required]" name="itree" optional="False" type="data" /> | |
| 30 <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] Reference taxonomic table that maps every OTU-ID into a taxonomic lineage string. [required]" name="ireferencetaxonomy" optional="False" type="data" /> | |
| 31 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> | |
| 32 | |
| 33 </inputs> | |
| 34 | |
| 35 <outputs> | |
| 36 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification" /> | |
| 37 | |
| 38 </outputs> | |
| 39 | |
| 40 <help><![CDATA[ | |
| 41 Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny. | |
| 42 ############################################################### | |
| 43 | |
| 44 | |
| 45 Experimental: Use the resulting tree from 'sepp' and find closest OTU-ID | |
| 46 for every inserted fragment. Then, look up the reference lineage string in | |
| 47 the reference taxonomy. | |
| 48 | |
| 49 Parameters | |
| 50 ---------- | |
| 51 representative_sequences : FeatureData[Sequence] | |
| 52 The sequences used for a 'sepp' run to produce the 'tree'. | |
| 53 tree : Phylogeny[Rooted] | |
| 54 The tree resulting from inserting fragments into a reference phylogeny, | |
| 55 i.e. the output of function 'sepp' | |
| 56 reference_taxonomy : FeatureData[Taxonomy] | |
| 57 Reference taxonomic table that maps every OTU-ID into a taxonomic | |
| 58 lineage string. | |
| 59 | |
| 60 Returns | |
| 61 ------- | |
| 62 classification : FeatureData[Taxonomy] | |
| 63 Taxonomic lineages for inserted fragments. | |
| 64 ]]></help> | |
| 65 <macros> | |
| 66 <import>qiime_citation.xml</import> | |
| 67 </macros> | |
| 68 <expand macro="qiime_citation"/> | |
| 69 </tool> |