Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_gneiss_assign-ids.xml @ 14:a0a8d77a991c draft
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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:51:29 +0000 |
parents | f190567fe3f6 |
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13:887cd4ad8e16 | 14:a0a8d77a991c |
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1 <?xml version="1.0" ?> | 1 <?xml version="1.0" ?> |
2 <tool id="qiime_gneiss_assign-ids" name="qiime gneiss assign-ids" version="2019.7"> | 2 <tool id="qiime_gneiss_assign-ids" name="qiime gneiss assign-ids" |
3 <description> - Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.</description> | 3 version="2020.8"> |
4 <requirements> | 4 <description>Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.</description> |
5 <requirement type="package" version="2019.7">qiime2</requirement> | 5 <requirements> |
6 </requirements> | 6 <requirement type="package" version="2020.8">qiime2</requirement> |
7 <command><![CDATA[ | 7 </requirements> |
8 <command><![CDATA[ | |
8 qiime gneiss assign-ids | 9 qiime gneiss assign-ids |
9 | 10 |
10 --i-input-table=$iinputtable | 11 --i-input-table=$iinputtable |
12 | |
11 --i-input-tree=$iinputtree | 13 --i-input-tree=$iinputtree |
12 | 14 |
13 --o-output-table=ooutputtable | 15 --o-output-table=ooutputtable |
16 | |
14 --o-output-tree=ooutputtree | 17 --o-output-tree=ooutputtree |
18 | |
19 #if str($examples) != 'None': | |
20 --examples=$examples | |
21 #end if | |
22 | |
15 ; | 23 ; |
16 cp ooutputtable.qza $ooutputtable; | |
17 cp ooutputtree.qza $ooutputtree | 24 cp ooutputtree.qza $ooutputtree |
18 ]]></command> | 25 |
19 <inputs> | 26 ]]></command> |
20 <param format="qza,no_unzip.zip" label="--i-input-table: ARTIFACT FeatureTable[Frequency] The input table of counts. [required]" name="iinputtable" optional="False" type="data"/> | 27 <inputs> |
21 <param format="qza,no_unzip.zip" label="--i-input-tree: ARTIFACT Phylogeny[Rooted] The input tree with potential missing ids. [required]" name="iinputtree" optional="False" type="data"/> | 28 <param format="qza,no_unzip.zip" label="--i-input-table: ARTIFACT FeatureTable[Frequency] The input table of counts. [required]" name="iinputtable" optional="False" type="data" /> |
22 </inputs> | 29 <param format="qza,no_unzip.zip" label="--i-input-tree: ARTIFACT Phylogeny[Rooted] The input tree with potential missing ids. [required]" name="iinputtree" optional="False" type="data" /> |
23 <outputs> | 30 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> |
24 <data format="qza" label="${tool.name} on ${on_string}: outputtable.qza" name="ooutputtable"/> | 31 |
25 <data format="qza" label="${tool.name} on ${on_string}: outputtree.qza" name="ooutputtree"/> | 32 </inputs> |
26 </outputs> | 33 |
27 <help><![CDATA[ | 34 <outputs> |
35 <data format="qza" label="${tool.name} on ${on_string}: outputtable.qza" name="ooutputtable" /> | |
36 <data format="qza" label="${tool.name} on ${on_string}: outputtree.qza" name="ooutputtree" /> | |
37 | |
38 </outputs> | |
39 | |
40 <help><![CDATA[ | |
28 Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns. | 41 Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns. |
29 ########################################################################################################## | 42 ############################################################### |
43 | |
30 | 44 |
31 Assigns UUIDs to uniquely identify internal nodes in the tree. Also | 45 Assigns UUIDs to uniquely identify internal nodes in the tree. Also |
32 corrects for polytomies to create strictly bifurcating trees and aligns the | 46 corrects for polytomies to create strictly bifurcating trees and aligns the |
33 table columns with the tree tip names | 47 table columns with the tree tip names |
34 | 48 |
43 ------- | 57 ------- |
44 output_table : FeatureTable[Frequency] | 58 output_table : FeatureTable[Frequency] |
45 A table with features matching the tree tips. | 59 A table with features matching the tree tips. |
46 output_tree : Hierarchy | 60 output_tree : Hierarchy |
47 A tree with uniquely identifying ids. | 61 A tree with uniquely identifying ids. |
48 ]]></help> | 62 ]]></help> |
49 <macros> | 63 <macros> |
50 <import>qiime_citation.xml</import> | 64 <import>qiime_citation.xml</import> |
51 </macros> | 65 </macros> |
52 <expand macro="qiime_citation"/> | 66 <expand macro="qiime_citation"/> |
53 </tool> | 67 </tool> |