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comparison qiime2/qiime_composition_ancom.xml @ 4:71f124e02000 draft default tip

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:40:25 -0400
parents 149432539226
children
comparison
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3:eda5df31da55 4:71f124e02000
7 <command><![CDATA[ 7 <command><![CDATA[
8 qiime composition ancom 8 qiime composition ancom
9 9
10 --i-table=$itable 10 --i-table=$itable
11 11
12 #def list_dict_to_string(list_dict):
13 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
14 #for d in list_dict[1:]:
15 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
16 #end for
17 #return $file_list
18 #end def
19 12
20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --m-metadata-column="$mmetadatacolumn" 13
14 #if $metadatafile:
15 --m-metadata-file=$metadatafile
16 #end if
17
18
19
20 --m-metadata-column="$mmetadatacolumn"
21 21
22 #if str($pdifferencefunction) != 'None': 22 #if str($pdifferencefunction) != 'None':
23 --p-difference-function=$pdifferencefunction 23 --p-difference-function=$pdifferencefunction
24 #end if 24 #end if
25 25
33 && cp -r out/* '$ovisualization.files_path' 33 && cp -r out/* '$ovisualization.files_path'
34 && mv '$ovisualization.files_path/index.html' '$ovisualization' 34 && mv '$ovisualization.files_path/index.html' '$ovisualization'
35 ]]></command> 35 ]]></command>
36 <inputs> 36 <inputs>
37 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Composition] - The feature table to be used for ANCOM computation. [required]" name="itable" optional="False" type="data"/> 37 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Composition] - The feature table to be used for ANCOM computation. [required]" name="itable" optional="False" type="data"/>
38 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> 38
39 <param format="tabular" label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data"/> 39 <param label="--m-metadata-file METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" optional="True" />
40 </repeat> 40
41
41 <param label="--m-metadata-column: MetadataColumn[Categorical] - Column from metadata file or artifact viewable as metadata. The categorical sample metadata column to test for differential abundance across. [required]" name="mmetadatacolumn" optional="False" type="text"/> 42 <param label="--m-metadata-column: MetadataColumn[Categorical] - Column from metadata file or artifact viewable as metadata. The categorical sample metadata column to test for differential abundance across. [required]" name="mmetadatacolumn" optional="False" type="text"/>
42 <param label="--p-difference-function: " name="pdifferencefunction" optional="True" type="select"> 43 <param label="--p-difference-function: " name="pdifferencefunction" optional="True" type="select">
43 <option selected="True" value="None">Selection is Optional</option> 44 <option selected="True" value="None">Selection is Optional</option>
44 <option value="mean_difference">mean_difference</option> 45 <option value="mean_difference">mean_difference</option>
45 <option value="f_statistic">f_statistic</option> 46 <option value="f_statistic">f_statistic</option>