Mercurial > repos > florianbegusch > qiime2_suite

comparison qiime2/qiime_emperor_biplot.xml @ 4:914fa4daf16a draft

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Fixes
author florianbegusch
date Wed, 31 Jul 2019 03:06:00 -0400
parents 51025741f326
children de4c22a52df4
comparison
equal deleted inserted replaced
3:558645416841 4:914fa4daf16a
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 $file_list
19 #end def 20 #end def
20 21 --m-sample-metadata-file=$list_dict_to_string_sample_mdata($m_sample_metadatafile)
21 #if $m_sample_metadatafile:
22 --m-sample-metadata-file=$list_dict_to_string($m_sample_metadatafile)
23 #end if 22 #end if
24 23
25 if $m_feature_metadatafile: 24
26 --m-feature-metadata-file=$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)
27 #end if 35 #end if
36
28 37
29 38
30 #if $pignoremissingsamples: 39 #if $pignoremissingsamples:
31 --p-ignore-missing-samples 40 --p-ignore-missing-samples
32 #end if 41 #end if
44 <inputs> 53 <inputs>
45 <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"/>
46 <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"/>
47 <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"/>
48 57
49 <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]">
50 <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" />
51 </repeat> 60 </repeat>
52 61
53 <repeat name="m_feature_metadatafile" optional="True" title="--m-metadata-file"> 62 <repeat name="m_feature_metadatafile" optional="True" title="--m-feature-metadata-file">
54 <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" />
55 </repeat> 64 </repeat>
56 65
57 </inputs> 66 </inputs>
58 <outputs> 67 <outputs>