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comparison qiime2/qiime_quality-control_evaluate-composition.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
equal deleted inserted replaced
3:eda5df31da55 4:71f124e02000
8 qiime quality-control evaluate-composition 8 qiime quality-control evaluate-composition
9 9
10 --i-expected-features=$iexpectedfeatures 10 --i-expected-features=$iexpectedfeatures
11 --i-observed-features=$iobservedfeatures 11 --i-observed-features=$iobservedfeatures
12 12
13 #if $input_files_mmetadatafile: 13
14 #def list_dict_to_string(list_dict): 14 #if $metadatafile:
15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 15 --m-metadata-file=$metadatafile
16 #for d in list_dict[1:]:
17 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
18 #end for
19 #return $file_list
20 #end def
21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
22 #end if 16 #end if
23 17
24 18
25 #if $pdepth: 19 #if str($pdepth):
26 --p-depth=$pdepth 20 --p-depth=$pdepth
27 #end if 21 #end if
28 22
29 #if str($ppalette) != 'None': 23 #if str($ppalette) != 'None':
30 --p-palette=$ppalette 24 --p-palette=$ppalette
56 50
57 #if $pplotobservedfeatures: 51 #if $pplotobservedfeatures:
58 --p-plot-observed-features 52 --p-plot-observed-features
59 #end if 53 #end if
60 54
61 #if $pplotobservedfeaturesratio: 55 #if $pnoplotobservedfeaturesratio:
62 --p-plot-observed-features-ratio 56 --p-no-plot-observed-features-ratio
63 #end if 57 #end if
64 58
65 #if str($mmetadatacolumn): 59 #if str($mmetadatacolumn):
66 --m-metadata-column="$mmetadatacolumn" 60 --m-metadata-column="$mmetadatacolumn"
67 #end if 61 #end if
105 <param label="--p-plot-jaccard: --p-no-plot-jaccard Plot expected vs. observed Jaccard distances scores on score plot. [default: False]" name="pplotjaccard" selected="False" type="boolean"/> 99 <param label="--p-plot-jaccard: --p-no-plot-jaccard Plot expected vs. observed Jaccard distances scores on score plot. [default: False]" name="pplotjaccard" selected="False" type="boolean"/>
106 <param label="--p-plot-observed-features: --p-no-plot-observed-features Plot observed features count on score plot. [default: False]" name="pplotobservedfeatures" selected="False" type="boolean"/> 100 <param label="--p-plot-observed-features: --p-no-plot-observed-features Plot observed features count on score plot. [default: False]" name="pplotobservedfeatures" selected="False" type="boolean"/>
107 <param label="--p-no-plot-observed-features-ratio: Do not plot ratio of observed:expected features on score plot. [default: False]" name="pnoplotobservedfeaturesratio" selected="False" type="boolean"/> 101 <param label="--p-no-plot-observed-features-ratio: Do not plot ratio of observed:expected features on score plot. [default: False]" name="pnoplotobservedfeaturesratio" selected="False" type="boolean"/>
108 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Optional sample metadata that maps observed-features sample IDs to expected-features sample IDs. [optional]" name="mmetadatacolumn" optional="True" type="text"/> 102 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Optional sample metadata that maps observed-features sample IDs to expected-features sample IDs. [optional]" name="mmetadatacolumn" optional="True" type="text"/>
109 103
110 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> 104 <param label="--m-metadata-file METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" />
111 <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" /> 105
112 </repeat>
113 106
114 </inputs> 107 </inputs>
115 <outputs> 108 <outputs>
116 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 109 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
117 </outputs> 110 </outputs>