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comparison qiime2/qiime_gneiss_balance-taxonomy.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 gneiss balance-taxonomy 8 qiime gneiss balance-taxonomy
9 9
10
11 #if str( $id_to_taxonomy_fp.selector ) == 'history'
12 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
13 --i-taxonomy '$tax'
14 #else:
15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
16 --i-taxonomy '$tax'
17 #end if
18
19
10 --i-table=$itable 20 --i-table=$itable
11 --i-tree=$itree 21 --i-tree=$itree
12 --i-taxonomy=$itaxonomy
13 --p-balance-name="$pbalancename" 22 --p-balance-name="$pbalancename"
14 23
15 24
16 #if $input_files_mmetadatafile: 25
17 #def list_dict_to_string(list_dict): 26 #if $metadatafile:
18 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 27 --m-metadata-file=$metadatafile
19 #for d in list_dict[1:]:
20 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
21 #end for
22 #return $file_list
23 #end def
24 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
25 #end if 28 #end if
26 29
27 30
28 #if $ppseudocount: 31
32 #if str($ppseudocount):
29 --p-pseudocount=$ppseudocount 33 --p-pseudocount=$ppseudocount
30 #end if 34 #end if
31 35
32 #if $ptaxalevel: 36 #if str($ptaxalevel):
33 --p-taxa-level=$ptaxalevel 37 --p-taxa-level=$ptaxalevel
34 #end if 38 #end if
35 39
36 #if $pnfeatures: 40 #if str($pnfeatures):
37 --p-n-features=$pnfeatures 41 --p-n-features=$pnfeatures
38 #end if 42 #end if
39 43
40 #if str($pthreshold): 44 #if str($pthreshold):
41 --p-threshold="$pthreshold" 45 --p-threshold="$pthreshold"
49 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 53 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
50 && cp -r out/* '$ovisualization.files_path' 54 && cp -r out/* '$ovisualization.files_path'
51 && mv '$ovisualization.files_path/index.html' '$ovisualization' 55 && mv '$ovisualization.files_path/index.html' '$ovisualization'
52 ]]></command> 56 ]]></command>
53 <inputs> 57 <inputs>
58
59 <conditional name="id_to_taxonomy_fp" optional="True">
60 <param name="selector" type="select" label="Reference taxonomy to query">
61 <option value="cached">Public databases</option>
62 <option value="history">Databases from your history</option>
63 </param>
64 <when value="cached">
65 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
66 <options from_data_table="qiime_taxonomy" />
67 </param>
68 </when>
69 <when value="history">
70 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
71 </when>
72 </conditional>
73
54 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] A table of abundances. [required]" name="itable" optional="False" type="data"/> 74 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] A table of abundances. [required]" name="itable" optional="False" type="data"/>
55 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT The tree used to calculate the balances. Hierarchy [required]" name="itree" optional="False" type="data"/> 75 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT The tree used to calculate the balances. Hierarchy [required]" name="itree" optional="False" type="data"/>
56 <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomy information for the OTUs. [required]" name="itaxonomy" optional="False" type="data"/> 76 <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomy information for the OTUs. [required]" name="itaxonomy" optional="False" type="data"/>
57 <param label="--p-balance-name: TEXT Name of the balance to summarize. [required]" name="pbalancename" optional="False" type="text"/> 77 <param label="--p-balance-name: TEXT Name of the balance to summarize. [required]" name="pbalancename" optional="False" type="text"/>
58 <param label="--p-pseudocount: NUMBER The pseudocount to add to avoid division by zero. [default: 0.5]" name="ppseudocount" optional="True" type="float" value="0.5"/> 78 <param label="--p-pseudocount: NUMBER The pseudocount to add to avoid division by zero. [default: 0.5]" name="ppseudocount" optional="True" type="float" value="0.5"/>
59 <param label="--p-taxa-level: INTEGER Level of taxonomy to summarize. [default: 0]" name="ptaxalevel" optional="True" type="integer" value="0"/> 79 <param label="--p-taxa-level: INTEGER Level of taxonomy to summarize. [default: 0]" name="ptaxalevel" optional="True" type="integer" value="0"/>
60 <param label="--p-n-features: INTEGER The number of features to plot in the proportion plot. [default: 10]" name="pnfeatures" optional="True" type="integer" value="10"/> 80 <param label="--p-n-features: INTEGER The number of features to plot in the proportion plot. [default: 10]" name="pnfeatures" optional="True" type="integer" value="10"/>
61 <param label="--p-threshold: NUMBER A threshold to designate discrete categories for a numerical metadata column. This will split the numerical column values into two categories, values below the threshold, and values above the threshold. If not specified, this threshold will default to the mean. [optional]" name="pthreshold" optional="True" type="float"/> 81 <param label="--p-threshold: NUMBER A threshold to designate discrete categories for a numerical metadata column. This will split the numerical column values into two categories, values below the threshold, and values above the threshold. If not specified, this threshold will default to the mean. [optional]" name="pthreshold" optional="True" type="float"/>
62 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical | Numeric] Metadata column for plotting the balance (optional). [optional]" name="mmetadatacolumn" optional="True" type="text"/> 82 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical | Numeric] Metadata column for plotting the balance (optional). [optional]" name="mmetadatacolumn" optional="True" type="text"/>
63 83
64 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> 84 <param label="--m-metadata-file METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" optional="True" />
65 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
66 </repeat>
67 85
68 </inputs> 86 </inputs>
69 <outputs> 87 <outputs>
70 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 88 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
71 </outputs> 89 </outputs>