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comparison qiime2/qiime_emperor_procrustes-plot.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
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3:eda5df31da55 4:71f124e02000
6 </requirements> 6 </requirements>
7 <command><![CDATA[ 7 <command><![CDATA[
8 qiime emperor procrustes-plot 8 qiime emperor procrustes-plot
9 9
10 --i-reference-pcoa=$ireferencepcoa 10 --i-reference-pcoa=$ireferencepcoa
11
11 --i-other-pcoa=$iotherpcoa 12 --i-other-pcoa=$iotherpcoa
12 13
13 14
14 #if $input_files_mmetadatafile: 15 #if $input_files_mmetadatafile:
15 #def list_dict_to_string(list_dict): 16 #def list_dict_to_string(list_dict):
22 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) 23 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
23 #end if 24 #end if
24 25
25 26
26 27
28 #if '__sq__' in str($pcustomaxes):
29 #set $pcustomaxes_temp = $pcustomaxes.replace('__sq__', "'")
30 #set $pcustomaxes = $pcustomaxes_temp
31 #end if
32
33 #if '__cb__' in str($pcustomaxes):
34 #set $pcustomaxes_temp = $pcustomaxes.replace('__cb__', "]")
35 #set $pcustomaxes = $pcustomaxes_temp
36 #end if
37
27 #if str($pcustomaxes): 38 #if str($pcustomaxes):
28 --p-custom-axes="$pcustomaxes" 39 --p-custom-axes="$pcustomaxes"
29 #end if 40 #end if
41
42
43
30 44
31 #if $pignoremissingsamples: 45 #if $pignoremissingsamples:
32 --p-ignore-missing-samples 46 --p-ignore-missing-samples
33 #end if 47 #end if
34 48
42 <param format="qza,no_unzip.zip" label="--i-reference-pcoa: ARTIFACT PCoAResults The reference ordination matrix to be plotted. [required]" name="ireferencepcoa" optional="False" type="data"/> 56 <param format="qza,no_unzip.zip" label="--i-reference-pcoa: ARTIFACT PCoAResults The reference ordination matrix to be plotted. [required]" name="ireferencepcoa" optional="False" type="data"/>
43 <param format="qza,no_unzip.zip" label="--i-other-pcoa: ARTIFACT PCoAResults The 'other' ordination matrix to be plotted (the one that was fitted to the reference). [required]" name="iotherpcoa" optional="False" type="data"/> 57 <param format="qza,no_unzip.zip" label="--i-other-pcoa: ARTIFACT PCoAResults The 'other' ordination matrix to be plotted (the one that was fitted to the reference). [required]" name="iotherpcoa" optional="False" type="data"/>
44 <param label="--p-custom-axes: TEXT... List[Str] Numeric sample metadata columns that should be included as axes in the Emperor plot. [optional]" name="pcustomaxes" optional="True" type="text"/> 58 <param label="--p-custom-axes: TEXT... List[Str] Numeric sample metadata columns that should be included as axes in the Emperor plot. [optional]" name="pcustomaxes" optional="True" type="text"/>
45 <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"/> 59 <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"/>
46 60
47 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> 61 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]">
48 <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" /> 62 <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" />
49 </repeat> 63 </repeat>
50 64
51 </inputs> 65 </inputs>
52 <outputs> 66 <outputs>