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comparison qiime2/qiime_longitudinal_first-distances.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_first-distances" name="qiime longitudinal first-distances"
3 version="2020.8">
4 <description>Compute first distances or distance 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-distances
10
11 --i-distance-matrix=$idistancematrix
12 # if $input_files_mmetadatafile:
13 # def list_dict_to_string(list_dict):
14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
15 # for d in list_dict[1:]:
16 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
17 # end for
18 # return $file_list
19 # end def
20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
21 # end if
22
23 #if '__ob__' in str($pstatecolumn):
24 #set $pstatecolumn_temp = $pstatecolumn.replace('__ob__', '[')
25 #set $pstatecolumn = $pstatecolumn_temp
26 #end if
27 #if '__cb__' in str($pstatecolumn):
28 #set $pstatecolumn_temp = $pstatecolumn.replace('__cb__', ']')
29 #set $pstatecolumn = $pstatecolumn_temp
30 #end if
31 #if 'X' in str($pstatecolumn):
32 #set $pstatecolumn_temp = $pstatecolumn.replace('X', '\\')
33 #set $pstatecolumn = $pstatecolumn_temp
34 #end if
35 #if '__sq__' in str($pstatecolumn):
36 #set $pstatecolumn_temp = $pstatecolumn.replace('__sq__', "'")
37 #set $pstatecolumn = $pstatecolumn_temp
38 #end if
39 #if '__db__' in str($pstatecolumn):
40 #set $pstatecolumn_temp = $pstatecolumn.replace('__db__', '"')
41 #set $pstatecolumn = $pstatecolumn_temp
42 #end if
43
44 --p-state-column=$pstatecolumn
45
46
47 #if '__ob__' in str($pindividualidcolumn):
48 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
49 #set $pindividualidcolumn = $pindividualidcolumn_temp
50 #end if
51 #if '__cb__' in str($pindividualidcolumn):
52 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
53 #set $pindividualidcolumn = $pindividualidcolumn_temp
54 #end if
55 #if 'X' in str($pindividualidcolumn):
56 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
57 #set $pindividualidcolumn = $pindividualidcolumn_temp
58 #end if
59 #if '__sq__' in str($pindividualidcolumn):
60 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
61 #set $pindividualidcolumn = $pindividualidcolumn_temp
62 #end if
63 #if '__db__' in str($pindividualidcolumn):
64 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
65 #set $pindividualidcolumn = $pindividualidcolumn_temp
66 #end if
67
68 --p-individual-id-column=$pindividualidcolumn
69
70
71 #if str($pbaseline):
72 --p-baseline=$pbaseline
73 #end if
74 #if str($preplicatehandling) != 'None':
75 --p-replicate-handling=$preplicatehandling
76 #end if
77
78 --o-first-distances=ofirstdistances
79
80 #if str($examples) != 'None':
81 --examples=$examples
82 #end if
83
84 ;
85 cp ofirstdistances.qza $ofirstdistances
86
87 ]]></command>
88 <inputs>
89 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data" />
90 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
91 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata file containing arguments will be individual-id-column. merged) [required]" name="additional_input" optional="False" type="data" />
92 </repeat>
93 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text" />
94 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text" />
95 <param label="--p-baseline: NUMBER A value listed in the state-column metadata column against which all other states should be compared. Toggles calculation of static distances instead of first distances (which are calculated if no value is given for baseline). If a \'baseline\' value is provided, sample distances at each state are compared against the baseline state, instead of the previous state. Must be a value listed in the state-column. [optional]" name="pbaseline" optional="False" type="text" />
96 <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
97 <option selected="True" value="None">Selection is Optional</option>
98 <option value="error">error</option>
99 <option value="random">random</option>
100 <option value="drop">drop</option>
101 </param>
102 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
103
104 </inputs>
105
106 <outputs>
107 <data format="qza" label="${tool.name} on ${on_string}: firstdistances.qza" name="ofirstdistances" />
108
109 </outputs>
110
111 <help><![CDATA[
112 Compute first distances or distance from baseline between sequential states
113 ###############################################################
114
115 Calculates first distances between sequential states for samples collected
116 from individual subjects sampled repeatedly at two or more states. This
117 method is similar to the "first differences" method, except that it
118 requires a distance matrix as input and calculates first differences as
119 distances between successive states. Outputs a data series of first
120 distances for each individual subject at each sequential pair of states,
121 labeled by the SampleID of the second state (e.g., paired distances between
122 time 0 and time 1 would be labeled by the SampleIDs at time 1). This file
123 can be used as input to linear mixed effects models or other longitudinal
124 or diversity methods to compare changes in first distances across time or
125 among groups of subjects. Also supports distance from baseline (or other
126 static comparison state) by setting the "baseline" parameter.
127
128 Parameters
129 ----------
130 distance_matrix : DistanceMatrix
131 Matrix of distances between pairs of samples.
132 metadata : Metadata
133 Sample metadata file containing individual_id_column.
134 state_column : Str
135 Metadata column containing state (time) variable information.
136 individual_id_column : Str
137 Metadata column containing IDs for individual subjects.
138 baseline : Float, optional
139 A value listed in the state_column metadata column against which all
140 other states should be compared. Toggles calculation of static
141 distances instead of first distances (which are calculated if no value
142 is given for baseline). If a "baseline" value is provided, sample
143 distances at each state are compared against the baseline state,
144 instead of the previous state. Must be a value listed in the
145 state_column.
146 replicate_handling : Str % Choices('error', 'random', 'drop'), optional
147 Choose how replicate samples are handled. If replicates are detected,
148 "error" causes method to fail; "drop" will discard all replicated
149 samples; "random" chooses one representative at random from among
150 replicates.
151
152 Returns
153 -------
154 first_distances : SampleData[FirstDifferences]
155 Series of first distances.
156 ]]></help>
157 <macros>
158 <import>qiime_citation.xml</import>
159 </macros>
160 <expand macro="qiime_citation"/>
161 </tool>