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comparison qiime2/qiime_taxa_collapse.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_taxa_collapse" name="qiime taxa collapse" version="2019.7"> 2 <tool id="qiime_taxa_collapse" name="qiime taxa collapse"
3 <description> - Collapse features by their taxonomy at the specified level</description> 3 version="2020.8">
4 <requirements> 4 <description>Collapse features by their taxonomy at the specified level</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 taxa collapse 9 qiime taxa collapse
9
10 #if str( $id_to_taxonomy_fp.selector ) == 'history'
11 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
12 --i-taxonomy '$tax'
13 #else:
14 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
15 --i-taxonomy '$tax'
16 #end if
17
18 10
19 --i-table=$itable 11 --i-table=$itable
20 12
21 #if str($plevel): 13 --i-taxonomy=$itaxonomy
22 --p-level="$plevel" 14
15 --p-level=$plevel
16
17 --o-collapsed-table=ocollapsedtable
18
19 #if str($examples) != 'None':
20 --examples=$examples
23 #end if 21 #end if
24 22
25 --o-collapsed-table=ocollapsedtable
26 ; 23 ;
27 cp ocollapsedtable.qza $ocollapsedtable 24 cp ocollapsedtable.qza $ocollapsedtable
28 ]]></command>
29 <inputs>
30 25
31 <conditional name="id_to_taxonomy_fp" optional="True"> 26 ]]></command>
32 <param name="selector" type="select" label="Reference taxonomy to query"> 27 <inputs>
33 <option value="cached">Public databases</option> 28 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required]" name="itable" optional="False" type="data" />
34 <option value="history">Databases from your history</option> 29 <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required]" name="itaxonomy" optional="False" type="data" />
35 </param> 30 <param label="--p-level: INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required]" name="plevel" optional="False" type="text" />
36 <when value="cached"> 31 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
37 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True"> 32
38 <options from_data_table="qiime_taxonomy" /> 33 </inputs>
39 </param>
40 </when>
41 <when value="history">
42 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
43 </when>
44 </conditional>
45
46 34
47 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required]" name="itable" optional="False" type="data"/> 35 <outputs>
48 <param label="--p-level: INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required]" name="plevel" optional="False" value="" type="integer"/> 36 <data format="qza" label="${tool.name} on ${on_string}: collapsedtable.qza" name="ocollapsedtable" />
49 </inputs> 37
50 <outputs> 38 </outputs>
51 <data format="qza" label="${tool.name} on ${on_string}: collapsedtable.qza" name="ocollapsedtable"/> 39
52 </outputs> 40 <help><![CDATA[
53 <help><![CDATA[
54 Collapse features by their taxonomy at the specified level 41 Collapse features by their taxonomy at the specified level
55 ########################################################## 42 ###############################################################
56 43
57 Collapse groups of features that have the same taxonomic assignment through 44 Collapse groups of features that have the same taxonomic assignment through
58 the specified level. The frequencies of all features will be summed when 45 the specified level. The frequencies of all features will be summed when
59 they are collapsed. 46 they are collapsed.
60 47
75 Returns 62 Returns
76 ------- 63 -------
77 collapsed_table : FeatureTable[Frequency] 64 collapsed_table : FeatureTable[Frequency]
78 The resulting feature table, where all features are now taxonomic 65 The resulting feature table, where all features are now taxonomic
79 annotations with the user-specified number of levels. 66 annotations with the user-specified number of levels.
80 ]]></help> 67 ]]></help>
81 <macros> 68 <macros>
82 <import>qiime_citation.xml</import> 69 <import>qiime_citation.xml</import>
83 </macros> 70 </macros>
84 <expand macro="qiime_citation"/> 71 <expand macro="qiime_citation"/>
85 </tool> 72 </tool>