Mercurial > repos > florianbegusch > qiime2_wrappers

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 emperor biplot 8 qiime emperor biplot
9 9
10 --i-biplot=$ibiplot 10 --i-biplot=$ibiplot
11 11
12 12
13 #def list_dict_to_string(list_dict): 13 #if $m_sample_metadatafile:
14 #def list_dict_to_string_sample_mdata(list_dict):
14 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
15 #for d in list_dict[1:]: 16 #for d in list_dict[1:]:
16 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name') 17 #set $file_list = $file_list + ' --m-sample-metadata-file=' + d['additional_input'].__getattr__('file_name')
17 #end for 18 #end for
18 #return $file_list 19 #return $file_list
19 #end def 20 #end def
21 --m-sample-metadata-file=$list_dict_to_string_sample_mdata($m_sample_metadatafile)
22 #end if
20 23
21 --m-sample-metadata-file=$list_dict_to_string($m_sample_metadatafile) 24
22 --m-feature-metadata-file=$list_dict_to_string($m_feature_metadatafile) 25
26 #if $m_feature_metadatafile:
27 #def list_dict_to_string_feature_mdata(list_dict):
28 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
29 #for d in list_dict[1:]:
30 #set $file_list = $file_list + ' --m-feature-metadata-file=' + d['additional_input'].__getattr__('file_name')
31 #end for
32 #return $file_list
33 #end def
34 --m-feature-metadata-file=$list_dict_to_string_feature_mdata($m_feature_metadatafile)
35 #end if
36
23 37
24 38
25 #if $pignoremissingsamples: 39 #if $pignoremissingsamples:
26 --p-ignore-missing-samples 40 --p-ignore-missing-samples
27 #end if 41 #end if
28 42
29 #if $pnumberoffeatures: 43 #if str($pnumberoffeatures):
30 --p-number-of-features=$pnumberoffeatures 44 --p-number-of-features=$pnumberoffeatures
31 #end if 45 #end if
32 46
33 --o-visualization=ovisualization 47 --o-visualization=ovisualization
34 ; 48 ;
39 <inputs> 53 <inputs>
40 <param format="qza,no_unzip.zip" label="--i-biplot: ARTIFACT PCoAResults % Properties('biplot') The principal coordinates matrix to be plotted. [required]" name="ibiplot" optional="False" type="data"/> 54 <param format="qza,no_unzip.zip" label="--i-biplot: ARTIFACT PCoAResults % Properties('biplot') The principal coordinates matrix to be plotted. [required]" name="ibiplot" optional="False" type="data"/>
41 <param label="--p-ignore-missing-samples: --p-no-ignore-missing-samples This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: 'This sample has no metadata'. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]" name="pignoremissingsamples" selected="False" type="boolean"/> 55 <param label="--p-ignore-missing-samples: --p-no-ignore-missing-samples This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: 'This sample has no metadata'. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata. [default: False]" name="pignoremissingsamples" selected="False" type="boolean"/>
42 <param label="--p-number-of-features: INTEGER Range(1, None) The number of most important features (arrows) to display in the ordination. [default: 5]" name="pnumberoffeatures" optional="True" type="integer" min="1" value="5"/> 56 <param label="--p-number-of-features: INTEGER Range(1, None) The number of most important features (arrows) to display in the ordination. [default: 5]" name="pnumberoffeatures" optional="True" type="integer" min="1" value="5"/>
43 57
44 <repeat name="m_sample_metadatafile" optional="False" title="--m-metadata-file"> 58 <repeat name="m_sample_metadatafile" optional="False" title="--m-sample-metadata-file [required]">
45 <param label="--m-sample-metadata-file: (multiple arguments will be merged) The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> 59 <param label="--m-sample-metadata-file: (multiple arguments will be merged) The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
46 </repeat> 60 </repeat>
47 61
48 <repeat name="m_feature_metadatafile" optional="True" title="--m-metadata-file"> 62 <repeat name="m_feature_metadatafile" optional="True" title="--m-feature-metadata-file">
49 <param label="--m-feature-metadata-file: (multiple arguments will be merged) The feature metadata (useful to manipulate the arrows in the plot). [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> 63 <param label="--m-feature-metadata-file: (multiple arguments will be merged) The feature metadata (useful to manipulate the arrows in the plot). [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
50 </repeat> 64 </repeat>
51 65
52 </inputs> 66 </inputs>
53 <outputs> 67 <outputs>