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comparison qiime2-2020.8/qiime_longitudinal_first-differences.xml @ 20:d93d8888f0b0 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
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19:6c48f8d82424 20:d93d8888f0b0
1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_first-differences" name="qiime longitudinal first-differences"
3 version="2020.8">
4 <description>Compute first differences or difference from baseline between sequential states</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime longitudinal first-differences
10
11 #if str($itable) != 'None':
12 --i-table=$itable
13 #end if
14 # if $input_files_mmetadatafile:
15 # def list_dict_to_string(list_dict):
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 = $pindividualidcolumn_temp
60 #end if
61 #if '__sq__' in str($pindividualidcolumn):
62 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
63 #set $pindividualidcolumn = $pindividualidcolumn_temp
64 #end if
65 #if '__db__' in str($pindividualidcolumn):
66 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
67 #set $pindividualidcolumn = $pindividualidcolumn_temp
68 #end if
69
70 --p-individual-id-column=$pindividualidcolumn
71
72
73 --p-metric=$pmetric
74
75 #if str($preplicatehandling) != 'None':
76 --p-replicate-handling=$preplicatehandling
77 #end if
78
79 #if str($pbaseline):
80 --p-baseline=$pbaseline
81 #end if
82 --o-first-differences=ofirstdifferences
83
84 #if str($examples) != 'None':
85 --examples=$examples
86 #end if
87
88 ;
89 cp ofirstdifferences.qza $ofirstdifferences
90
91 ]]></command>
92 <inputs>
93 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table to optionally use for computing first differences. [optional]" name="itable" optional="False" type="data" />
94 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
95 <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" />
96 </repeat>
97 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text" />
98 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text" />
99 <param label="--p-metric: TEXT Numerical metadata or artifact column to test. [required]" name="pmetric" optional="False" type="text" />
100 <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
101 <option selected="True" value="None">Selection is Optional</option>
102 <option value="error">error</option>
103 <option value="random">random</option>
104 <option value="drop">drop</option>
105 </param>
106 <param label="--p-baseline: NUMBER A value listed in the state-column metadata column against which all other states should be compared. Toggles calculation of static differences instead of first differences (which are calculated if no value is given for baseline). If a \'baseline\' value is provided, sample differences at each state are compared against the baseline state, instead of the previous state. Must be a value listed in the state-column. [optional]" name="pbaseline" optional="False" type="text" />
107 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
108
109 </inputs>
110
111 <outputs>
112 <data format="qza" label="${tool.name} on ${on_string}: firstdifferences.qza" name="ofirstdifferences" />
113
114 </outputs>
115
116 <help><![CDATA[
117 Compute first differences or difference from baseline between sequential states
118 ###############################################################
119
120
121 Calculates first differences in "metric" between sequential states for
122 samples collected from individual subjects sampled repeatedly at two or
123 more states. First differences can be performed on a metadata column
124 (including artifacts that can be input as metadata) or a feature in a
125 feature table. Outputs a data series of first differences for each
126 individual subject at each sequential pair of states, labeled by the
127 SampleID of the second state (e.g., paired differences between time 0 and
128 time 1 would be labeled by the SampleIDs at time 1). This file can be used
129 as input to linear mixed effects models or other longitudinal or diversity
130 methods to compare changes in first differences across time or among groups
131 of subjects. Also supports differences from baseline (or other static
132 comparison state) by setting the "baseline" parameter.
133
134 Parameters
135 ----------
136 metadata : Metadata
137 Sample metadata file containing individual_id_column.
138 state_column : Str
139 Metadata column containing state (time) variable information.
140 individual_id_column : Str
141 Metadata column containing IDs for individual subjects.
142 metric : Str
143 Numerical metadata or artifact column to test.
144 replicate_handling : Str % Choices('error', 'random', 'drop'), optional
145 Choose how replicate samples are handled. If replicates are detected,
146 "error" causes method to fail; "drop" will discard all replicated
147 samples; "random" chooses one representative at random from among
148 replicates.
149 baseline : Float, optional
150 A value listed in the state_column metadata column against which all
151 other states should be compared. Toggles calculation of static
152 differences instead of first differences (which are calculated if no
153 value is given for baseline). If a "baseline" value is provided, sample
154 differences at each state are compared against the baseline state,
155 instead of the previous state. Must be a value listed in the
156 state_column.
157 table : FeatureTable[RelativeFrequency], optional
158 Feature table to optionally use for computing first differences.
159
160 Returns
161 -------
162 first_differences : SampleData[FirstDifferences]
163 Series of first differences.
164 ]]></help>
165 <macros>
166 <import>qiime_citation.xml</import>
167 </macros>
168 <expand macro="qiime_citation"/>
169 </tool>