Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_longitudinal_volatility.xml @ 14:a0a8d77a991c draft
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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:51:29 +0000 |
parents | f190567fe3f6 |
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13:887cd4ad8e16 | 14:a0a8d77a991c |
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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> |