Mercurial > repos > florianbegusch > qiime2_wrappers
comparison qiime2/qiime_gneiss_assign-ids.xml @ 0:51b9b6b57732 draft
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| author | florianbegusch |
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| date | Thu, 24 May 2018 05:21:07 -0400 |
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| -1:000000000000 | 0:51b9b6b57732 |
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| 1 <?xml version="1.0" ?> | |
| 2 <tool id="qiime_gneiss_assign-ids" name="qiime gneiss assign-ids" version="2018.4"> | |
| 3 <description> - Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2018.4">qiime2</requirement> | |
| 6 </requirements> | |
| 7 <command> | |
| 8 <![CDATA[ | |
| 9 qiime gneiss assign-ids --i-input-table=$iinputtable --i-input-tree=$iinputtree | |
| 10 | |
| 11 #if str($cmdconfig) != 'None': | |
| 12 --cmd-config=$cmdconfig | |
| 13 #end if | |
| 14 --o-output-tree=ooutputtree --o-output-table=ooutputtable; | |
| 15 | |
| 16 cp ooutputtree.qza $ooutputtree; | |
| 17 cp ooutputtable.qza $ooutputtable; | |
| 18 ]]> | |
| 19 </command> | |
| 20 <inputs> | |
| 21 <param format="qza,no_unzip.zip" label="--i-input-table: FeatureTable[Frequency] The input table of counts. [required]" name="iinputtable" optional="False" type="data"/> | |
| 22 <param format="qza,no_unzip.zip" label="--i-input-tree: Phylogeny[Rooted] The input tree with potential missing ids. [required]" name="iinputtree" optional="False" type="data"/> | |
| 23 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data format="qza" label="${tool.name} on ${on_string}: output-tree.qza" name="ooutputtree"/> | |
| 27 <data format="qza" label="${tool.name} on ${on_string}: output-table.qza" name="ooutputtable"/> | |
| 28 </outputs> | |
| 29 <help> | |
| 30 <![CDATA[ | |
| 31 Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns. | |
| 32 ----------------------------------------------------------------------------------------------------------- | |
| 33 | |
| 34 Assigns UUIDs to uniquely identify internal nodes in the tree. Also | |
| 35 corrects for polytomies to create strictly bifurcating trees and aligns the | |
| 36 table columns with the tree tip names | |
| 37 | |
| 38 Parameters | |
| 39 ---------- | |
| 40 input_table : FeatureTable[Frequency] | |
| 41 The input table of counts. | |
| 42 input_tree : Phylogeny[Rooted] | |
| 43 The input tree with potential missing ids. | |
| 44 | |
| 45 Returns | |
| 46 ------- | |
| 47 output_table : FeatureTable[Frequency] | |
| 48 A table with features matching the tree tips. | |
| 49 output_tree : Hierarchy | |
| 50 A tree with uniquely identifying ids. | |
| 51 ]]> | |
| 52 </help> | |
| 53 <macros> | |
| 54 <import>qiime_citation.xml</import> | |
| 55 </macros> | |
| 56 <expand macro="qiime_citation" /> | |
| 57 </tool> |