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comparison qiime2/qiime_taxa_collapse.xml @ 6:de4c22a52df4 draft

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:46:48 -0400
parents 370e0b6e9826
children f190567fe3f6
comparison
equal deleted inserted replaced
5:a025a4a89e07 6:de4c22a52df4
5 <requirement type="package" version="2019.4">qiime2</requirement> 5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements> 6 </requirements>
7 <command><![CDATA[ 7 <command><![CDATA[
8 qiime taxa collapse 8 qiime taxa collapse
9 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 --i-table=$itable 19 --i-table=$itable
11 --i-taxonomy=$itaxonomy 20
12 --p-level="$plevel" 21 #if str($plevel):
22 --p-level="$plevel"
23 #end if
13 24
14 --o-collapsed-table=ocollapsedtable 25 --o-collapsed-table=ocollapsedtable
15 ; 26 ;
16 cp ocollapsedtable.qza $ocollapsedtable 27 cp ocollapsedtable.qza $ocollapsedtable
17 ]]></command> 28 ]]></command>
18 <inputs> 29 <inputs>
30
31 <conditional name="id_to_taxonomy_fp" optional="True">
32 <param name="selector" type="select" label="Reference taxonomy to query">
33 <option value="cached">Public databases</option>
34 <option value="history">Databases from your history</option>
35 </param>
36 <when value="cached">
37 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
38 <options from_data_table="qiime_taxonomy" />
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
19 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required]" name="itable" optional="False" type="data"/> 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"/>
20 <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"/>
21 <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"/> 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"/>
22 </inputs> 49 </inputs>
23 <outputs> 50 <outputs>
24 <data format="qza" label="${tool.name} on ${on_string}: collapsedtable.qza" name="ocollapsedtable"/> 51 <data format="qza" label="${tool.name} on ${on_string}: collapsedtable.qza" name="ocollapsedtable"/>
25 </outputs> 52 </outputs>