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comparison qiime_longitudinal_first-distances.xml @ 0:09b7bcb72fa7 draft

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author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
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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>