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comparison qiime2/qiime_longitudinal_volatility.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_volatility" name="qiime longitudinal volatility" version="2019.7"> 2 <tool id="qiime_longitudinal_volatility" name="qiime longitudinal volatility"
3 <description> - Generate interactive volatility plot</description> 3 version="2020.8">
4 <requirements> 4 <description>Generate interactive volatility plot</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime longitudinal volatility 9 qiime longitudinal volatility
9 10
10 --p-state-column="$pstatecolumn"
11
12 #if str($itable) != 'None': 11 #if str($itable) != 'None':
13 --i-table=$itable 12 --i-table=$itable
14 #end if 13 #end if
15 14 # if $input_files_mmetadatafile:
16 15 # def list_dict_to_string(list_dict):
17 16 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
17 # for d in list_dict[1:]:
18 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
19 # end for
20 # return $file_list
21 # end def
22 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
23 # end if
24
25 #if '__ob__' in str($pstatecolumn):
26 #set $pstatecolumn_temp = $pstatecolumn.replace('__ob__', '[')
27 #set $pstatecolumn = $pstatecolumn_temp
28 #end if
29 #if '__cb__' in str($pstatecolumn):
30 #set $pstatecolumn_temp = $pstatecolumn.replace('__cb__', ']')
31 #set $pstatecolumn = $pstatecolumn_temp
32 #end if
33 #if 'X' in str($pstatecolumn):
34 #set $pstatecolumn_temp = $pstatecolumn.replace('X', '\\')
35 #set $pstatecolumn = $pstatecolumn_temp
36 #end if
37 #if '__sq__' in str($pstatecolumn):
38 #set $pstatecolumn_temp = $pstatecolumn.replace('__sq__', "'")
39 #set $pstatecolumn = $pstatecolumn_temp
40 #end if
41 #if '__db__' in str($pstatecolumn):
42 #set $pstatecolumn_temp = $pstatecolumn.replace('__db__', '"')
43 #set $pstatecolumn = $pstatecolumn_temp
44 #end if
45
46 --p-state-column=$pstatecolumn
47
48
49 #if '__ob__' in str($pindividualidcolumn):
50 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
51 #set $pindividualidcolumn = $pindividualidcolumn_temp
52 #end if
53 #if '__cb__' in str($pindividualidcolumn):
54 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
55 #set $pindividualidcolumn = $pindividualidcolumn_temp
56 #end if
57 #if 'X' in str($pindividualidcolumn):
58 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
59 #set $pindividualidcolumn = $pindividualidcolumn_temp
60 #end if
18 #if '__sq__' in str($pindividualidcolumn): 61 #if '__sq__' in str($pindividualidcolumn):
19 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'") 62 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
20 #set $pindividualidcolumn = $pindividualidcolumn_temp 63 #set $pindividualidcolumn = $pindividualidcolumn_temp
21 #end if 64 #end if
65 #if '__db__' in str($pindividualidcolumn):
66 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
67 #set $pindividualidcolumn = $pindividualidcolumn_temp
68 #end if
22 69
23 #if str($pindividualidcolumn): 70 #if str($pindividualidcolumn):
24 --p-individual-id-column="$pindividualidcolumn" 71 --p-individual-id-column=$pindividualidcolumn
25 #end if 72 #end if
26 73
27 74 #if '__ob__' in str($pdefaultgroupcolumn):
75 #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__ob__', '[')
76 #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
77 #end if
78 #if '__cb__' in str($pdefaultgroupcolumn):
79 #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__cb__', ']')
80 #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
81 #end if
82 #if 'X' in str($pdefaultgroupcolumn):
83 #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('X', '\\')
84 #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
85 #end if
86 #if '__sq__' in str($pdefaultgroupcolumn):
87 #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__sq__', "'")
88 #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
89 #end if
90 #if '__db__' in str($pdefaultgroupcolumn):
91 #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__db__', '"')
92 #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
93 #end if
28 94
29 #if str($pdefaultgroupcolumn): 95 #if str($pdefaultgroupcolumn):
30 --p-default-group-column="$pdefaultgroupcolumn" 96 --p-default-group-column=$pdefaultgroupcolumn
31 #end if 97 #end if
32 98
33 #if str($pdefaultmetric): 99 #if str($pdefaultmetric):
34 --p-default-metric="$pdefaultmetric" 100 --p-default-metric=$pdefaultmetric
35 #end if 101 #end if
36
37 #if str($pyscale) != 'None': 102 #if str($pyscale) != 'None':
38 --p-yscale=$pyscale 103 --p-yscale=$pyscale
39 #end if 104 #end if
40
41
42 #if $input_files_mmetadatafile:
43 #def list_dict_to_string(list_dict):
44 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
45 #for d in list_dict[1:]:
46 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
47 #end for
48 #return $file_list
49 #end def
50 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
51 #end if
52
53 105
54 --o-visualization=ovisualization 106 --o-visualization=ovisualization
55 ; 107
56 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 108 #if str($examples) != 'None':
57 && cp -r out/* '$ovisualization.files_path' 109 --examples=$examples
58 && mv '$ovisualization.files_path/index.html' '$ovisualization'; 110 #end if
59 ]]></command> 111
60 <inputs> 112 ;
61 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text"/> 113 cp odistancematrix.qza $odistancematrix
62 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing metrics. [optional]" name="itable" optional="True" type="data"/> 114
63 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [optional]" name="pindividualidcolumn" optional="True" type="text"/> 115 ;
64 <param label="--p-default-group-column: TEXT The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization). [optional]" name="pdefaultgroupcolumn" optional="True" type="text"/> 116 qiime tools export ovisualization.qzv --output-path out
65 <param label="--p-default-metric: TEXT Numeric metadata or artifact column to test by default (all numeric metadata columns will be available in the visualization). [optional]" name="pdefaultmetric" optional="True" type="text"/> 117 && mkdir -p '$ovisualization.files_path'
66 <param label="--p-yscale: " name="pyscale" optional="True" type="select"> 118 && cp -r out/* '$ovisualization.files_path'
67 <option selected="True" value="None">Selection is Optional</option> 119 && mv '$ovisualization.files_path/index.html' '$ovisualization'
68 <option value="linear">linear</option> 120
69 <option value="pow">pow</option> 121 ;
70 <option value="sqrt">sqrt</option> 122 qiime tools export ovisualization.qzv --output-path out
71 <option value="log">log</option> 123 && mkdir -p '$ovisualization.files_path'
72 </param> 124 && cp -r out/* '$ovisualization.files_path'
73 125 && mv '$ovisualization.files_path/index.html' '$ovisualization'
74 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]"> 126
75 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> 127 ;
76 </repeat> 128 qiime tools export ovisualization.qzv --output-path out
77 129 && mkdir -p '$ovisualization.files_path'
78 </inputs> 130 && cp -r out/* '$ovisualization.files_path'
79 <outputs> 131 && mv '$ovisualization.files_path/index.html' '$ovisualization'
80 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 132
81 </outputs> 133 ;
82 <help><![CDATA[ 134 qiime tools export ovisualization.qzv --output-path out
135 && mkdir -p '$ovisualization.files_path'
136 && cp -r out/* '$ovisualization.files_path'
137 && mv '$ovisualization.files_path/index.html' '$ovisualization'
138
139 ]]></command>
140 <inputs>
141 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing metrics. [optional]" name="itable" optional="False" type="data" />
142 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
143 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata file containing arguments will be individual-id-column. merged) [required]" name="additional_input" optional="False" type="data" />
144 </repeat>
145 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text" />
146 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [optional]" name="pindividualidcolumn" optional="False" type="text" />
147 <param label="--p-default-group-column: TEXT The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization). [optional]" name="pdefaultgroupcolumn" optional="False" type="text" />
148 <param label="--p-default-metric: TEXT Numeric metadata or artifact column to test by default (all numeric metadata columns will be available in the visualization). [optional]" name="pdefaultmetric" optional="False" type="text" />
149 <param label="--p-yscale: " name="pyscale" optional="True" type="select">
150 <option selected="True" value="None">Selection is Optional</option>
151 <option value="linear">linear</option>
152 <option value="pow">pow</option>
153 <option value="sqrt">sqrt</option>
154 <option value="log">log</option>
155 </param>
156 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
157
158 </inputs>
159
160 <outputs>
161 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
162
163 </outputs>
164
165 <help><![CDATA[
83 Generate interactive volatility plot 166 Generate interactive volatility plot
84 #################################### 167 ###############################################################
85 168
86 Generate an interactive control chart depicting the longitudinal volatility 169 Generate an interactive control chart depicting the longitudinal volatility
87 of sample metadata and/or feature frequencies across time (as set using the 170 of sample metadata and/or feature frequencies across time (as set using the
88 "state_column" parameter). Any numeric metadata column (and metadata- 171 "state_column" parameter). Any numeric metadata column (and metadata-
89 transformable artifacts, e.g., alpha diversity results) can be plotted on 172 transformable artifacts, e.g., alpha diversity results) can be plotted on
115 y-axis scaling strategy to apply. 198 y-axis scaling strategy to apply.
116 199
117 Returns 200 Returns
118 ------- 201 -------
119 visualization : Visualization 202 visualization : Visualization
120 ]]></help> 203 ]]></help>
121 <macros> 204 <macros>
122 <import>qiime_citation.xml</import> 205 <import>qiime_citation.xml</import>
123 </macros> 206 </macros>
124 <expand macro="qiime_citation"/> 207 <expand macro="qiime_citation"/>
125 </tool> 208 </tool>