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comparison qiime2/qiime_longitudinal_first-distances.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_first-distances" name="qiime longitudinal first-distances" version="2019.4">
3 <description> - Compute first distances or distance from baseline between sequential states</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime longitudinal first-distances
9
10 --i-distance-matrix=$idistancematrix
11 --p-state-column="$pstatecolumn"
12 --p-individual-id-column="$pindividualidcolumn"
13
14 #if str($pbaseline):
15 --p-baseline="$pbaseline"
16 #end if
17
18 #if str($preplicatehandling) != 'None':
19 --p-replicate-handling=$preplicatehandling
20 #end if
21
22
23 #if $input_files_mmetadatafile:
24 #def list_dict_to_string(list_dict):
25 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
26 #for d in list_dict[1:]:
27 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
28 #end for
29 #return $file_list
30 #end def
31 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
32 #end if
33
34
35 --o-first-distances=ofirstdistances
36 ;
37 cp ofirstdistances.qza $ofirstdistances
38 ]]></command>
39 <inputs>
40 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
41 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text"/>
42 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text"/>
43 <param label="--p-baseline: NUMBER A value listed in the state-column metadata column against which all other states should be compared. Toggles calculation of static distances instead of first distances (which are calculated if no value is given for baseline). If a 'baseline' value is provided, sample distances at each state are compared against the baseline state, instead of the previous state. Must be a value listed in the state-column. [optional]" name="pbaseline" optional="True" type="float"/>
44 <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
45 <option selected="True" value="None">Selection is Optional</option>
46 <option value="error">error</option>
47 <option value="random">random</option>
48 <option value="drop">drop</option>
49 </param>
50
51 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
52 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
53 </repeat>
54
55 </inputs>
56 <outputs>
57 <data format="qza" label="${tool.name} on ${on_string}: firstdistances.qza" name="ofirstdistances"/>
58 </outputs>
59 <help><![CDATA[
60 Compute first distances or distance from baseline between sequential states
61 ###########################################################################
62
63 Calculates first distances between sequential states for samples collected
64 from individual subjects sampled repeatedly at two or more states. This
65 method is similar to the "first differences" method, except that it
66 requires a distance matrix as input and calculates first differences as
67 distances between successive states. Outputs a data series of first
68 distances for each individual subject at each sequential pair of states,
69 labeled by the SampleID of the second state (e.g., paired distances between
70 time 0 and time 1 would be labeled by the SampleIDs at time 1). This file
71 can be used as input to linear mixed effects models or other longitudinal
72 or diversity methods to compare changes in first distances across time or
73 among groups of subjects. Also supports distance from baseline (or other
74 static comparison state) by setting the "baseline" parameter.
75
76 Parameters
77 ----------
78 distance_matrix : DistanceMatrix
79 Matrix of distances between pairs of samples.
80 metadata : Metadata
81 Sample metadata file containing individual_id_column.
82 state_column : Str
83 Metadata column containing state (time) variable information.
84 individual_id_column : Str
85 Metadata column containing IDs for individual subjects.
86 baseline : Float, optional
87 A value listed in the state_column metadata column against which all
88 other states should be compared. Toggles calculation of static
89 distances instead of first distances (which are calculated if no value
90 is given for baseline). If a "baseline" value is provided, sample
91 distances at each state are compared against the baseline state,
92 instead of the previous state. Must be a value listed in the
93 state_column.
94 replicate_handling : Str % Choices('error', 'random', 'drop'), optional
95 Choose how replicate samples are handled. If replicates are detected,
96 "error" causes method to fail; "drop" will discard all replicated
97 samples; "random" chooses one representative at random from among
98 replicates.
99
100 Returns
101 -------
102 first_distances : SampleData[FirstDifferences]
103 Series of first distances.
104 ]]></help>
105 <macros>
106 <import>qiime_citation.xml</import>
107 </macros>
108 <expand macro="qiime_citation"/>
109 </tool>