|
0
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_longitudinal_first-distances" name="qiime longitudinal first-distances" version="2018.4">
|
|
|
3 <description> - Compute first distances or distance from baseline between sequential states</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2018.4">qiime2</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command>
|
|
|
8 <![CDATA[
|
|
|
9 qiime longitudinal first-distances --p-state-column="$pstatecolumn" --p-individual-id-column="$pindividualidcolumn"
|
|
|
10
|
|
|
11 #def list_dict_to_string(list_dict):
|
|
|
12 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
|
|
|
13 #for d in list_dict[1:]:
|
|
|
14 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
|
|
|
15 #end for
|
|
|
16 #return $file_list
|
|
|
17 #end def
|
|
|
18
|
|
|
19
|
|
|
20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --i-distance-matrix=$idistancematrix
|
|
|
21 #if str($cmdconfig) != 'None':
|
|
|
22 --cmd-config=$cmdconfig
|
|
|
23 #end if
|
|
|
24 --o-first-distances=ofirstdistances
|
|
|
25 #if str($preplicatehandling) != 'None':
|
|
|
26 --p-replicate-handling=$preplicatehandling
|
|
|
27 #end if
|
|
|
28
|
|
|
29 #if str($pbaseline):
|
|
|
30 --p-baseline="$pbaseline"
|
|
|
31 #end if
|
|
|
32 ;
|
|
|
33
|
|
|
34 cp ofirstdistances.qza $ofirstdistances;
|
|
|
35 ]]>
|
|
|
36 </command>
|
|
|
37 <inputs>
|
|
|
38 <param format="qza,no_unzip.zip" label="--i-distance-matrix: DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
|
|
|
39
|
|
|
40 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
|
|
|
41 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. Sample metadata file containing individual_id_column. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
|
|
|
42 </repeat>
|
|
|
43
|
|
|
44 <param label="--p-state-column: Metadata column containing state (e.g., Time) across which samples are paired. [required]" name="pstatecolumn" optional="False" type="text"/>
|
|
|
45 <param label="--p-individual-id-column: Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text"/>
|
|
|
46
|
|
|
47 <param label="--p-replicate-handling: Choose how replicate samples are handled. If
|
|
|
48 replicates are detected, 'error' causes
|
|
|
49 method to fail; 'drop' will discard all
|
|
|
50 replicated samples; 'random' chooses one
|
|
|
51 representative at random from among
|
|
|
52 replicates. [default: error]" name="preplicatehandling" optional="True" type="select">
|
|
|
53 <option selected="True" value="None">Selection is Optional</option>
|
|
|
54 <option value="error">error</option>
|
|
|
55 <option value="random">random</option>
|
|
|
56 <option value="drop">drop</option>
|
|
|
57 </param>
|
|
|
58
|
|
|
59 <param label="--p-baseline: 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="text"/>
|
|
|
60
|
|
|
61 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
|
|
|
62 </inputs>
|
|
|
63 <outputs>
|
|
|
64 <data format="qza" label="${tool.name} on ${on_string}: firstdistances.qza" name="ofirstdistances"/>
|
|
|
65 </outputs>
|
|
|
66 <help>
|
|
|
67 <![CDATA[
|
|
|
68 Compute first distances or distance from baseline between sequential states
|
|
|
69 ----------------------------------------------------------------------------
|
|
|
70
|
|
|
71 Calculates first distances between sequential states for samples collected
|
|
|
72 from individual subjects sampled repeatedly at two or more states. This
|
|
|
73 method is similar to the "first differences" method, except that it
|
|
|
74 requires a distance matrix as input and calculates first differences as
|
|
|
75 distances between successive states. Outputs a data series of first
|
|
|
76 distances for each individual subject at each sequential pair of states,
|
|
|
77 labeled by the SampleID of the second state (e.g., paired distances between
|
|
|
78 time 0 and time 1 would be labeled by the SampleIDs at time 1). This file
|
|
|
79 can be used as input to linear mixed effects models or other longitudinal
|
|
|
80 or diversity methods to compare changes in first distances across time or
|
|
|
81 among groups of subjects. Also supports distance from baseline (or other
|
|
|
82 static comparison state) by setting the "baseline" parameter.
|
|
|
83
|
|
|
84 Parameters
|
|
|
85 ----------
|
|
|
86 distance_matrix : DistanceMatrix
|
|
|
87 Matrix of distances between pairs of samples.
|
|
|
88 metadata : Metadata
|
|
|
89 Sample metadata file containing individual_id_column.
|
|
|
90 state_column : Str
|
|
|
91 Metadata column containing state (e.g., Time) across which samples are
|
|
|
92 paired.
|
|
|
93 individual_id_column : Str
|
|
|
94 Metadata column containing IDs for individual subjects.
|
|
|
95 baseline : Float, optional
|
|
|
96 A value listed in the state_column metadata column against which all
|
|
|
97 other states should be compared. Toggles calculation of static
|
|
|
98 distances instead of first distances (which are calculated if no value
|
|
|
99 is given for baseline). If a "baseline" value is provided, sample
|
|
|
100 distances at each state are compared against the baseline state,
|
|
|
101 instead of the previous state. Must be a value listed in the
|
|
|
102 state_column.
|
|
|
103 replicate_handling : Str % Choices({'drop', 'error', 'random'}), optional
|
|
|
104 Choose how replicate samples are handled. If replicates are detected,
|
|
|
105 "error" causes method to fail; "drop" will discard all replicated
|
|
|
106 samples; "random" chooses one representative at random from among
|
|
|
107 replicates.
|
|
|
108
|
|
|
109 Returns
|
|
|
110 -------
|
|
|
111 first_distances : SampleData[FirstDifferences]
|
|
|
112 Series of first distances.
|
|
|
113 ]]>
|
|
|
114 </help>
|
|
|
115 </tool>
|
