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comparison qiime2/qiime_longitudinal_first-differences.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_first-differences" name="qiime longitudinal first-differences" version="2018.4">
3 <description> - Compute first differences or difference from baseline between sequential states</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9
10 qiime longitudinal first-differences --p-state-column="$pstatecolumn"
11
12 #if '__pd__' in str($pindividualidcolumn):
13 #set $pwhere_temp = $pindividualidcolumn.replace('__pd__', "#")
14 #set $pindividualidcolumn = $pwhere_temp
15 #end if
16
17 #def list_dict_to_string(list_dict):
18 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
19 #for d in list_dict[1:]:
20 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
21 #end for
22 #return $file_list
23 #end def
24
25
26 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --p-individual-id-column="$pindividualidcolumn" --p-metric="$pmetric"
27 #if str($itable) != 'None':
28 --i-table=$itable
29 #end if
30
31 #if str($cmdconfig) != 'None':
32 --cmd-config=$cmdconfig
33 #end if
34
35 #if str($preplicatehandling) != 'None':
36 --p-replicate-handling=$preplicatehandling
37 #end if
38 --o-first-differences=ofirstdifferences
39 #if str($pbaseline):
40 --p-baseline="$pbaseline"
41 #end if
42 ;
43 cp ofirstdifferences.qza $ofirstdifferences;
44 ]]>
45 </command>
46 <inputs>
47 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
48 <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" />
49 </repeat>
50
51 <param label="--p-state-column: Metadata column containing state (e.g., Time) across which samples are paired. [required]" name="pstatecolumn" optional="False" type="text"/>
52 <param label="--p-individual-id-column: Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text"/>
53
54 <param label="--p-metric: Numerical metadata or artifact column to test. [required]" name="pmetric" optional="False" type="text"/>
55
56 <param label="--p-replicate-handling: Choose how replicate samples are handled. If
57 replicates are detected, 'error' causes
58 method to fail; 'drop'' will discard all
59 replicated samples; 'random' chooses one
60 representative at random from among
61 replicates. [default: error]" name="preplicatehandling" optional="True" type="select">
62 <option selected="True" value="None">Selection is Optional</option>
63 <option value="error">error</option>
64 <option value="random">random</option>
65 <option value="drop">drop</option>
66 </param>
67
68 <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 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="True" type="text"/>
69
70 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[RelativeFrequency] Feature table to optionally use for computing first differences. [optional]" name="itable" optional="True" type="data"/>
71
72 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
73 </inputs>
74 <outputs>
75 <data format="qza" label="${tool.name} on ${on_string}: first-differences.qza" name="ofirstdifferences"/>
76 </outputs>
77 <help>
78 <![CDATA[
79 Compute first differences or difference from baseline between sequential states
80 --------------------------------------------------------------------------------
81
82 Calculates first differences in "metric" between sequential states for
83 samples collected from individual subjects sampled repeatedly at two or
84 more states. First differences can be performed on a metadata column
85 (including artifacts that can be input as metadata) or a feature in a
86 feature table. Outputs a data series of first differences for each
87 individual subject at each sequential pair of states, labeled by the
88 SampleID of the second state (e.g., paired differences between time 0 and
89 time 1 would be labeled by the SampleIDs at time 1). This file can be used
90 as input to linear mixed effects models or other longitudinal or diversity
91 methods to compare changes in first differences across time or among groups
92 of subjects. Also supports differences from baseline (or other static
93 comparison state) by setting the "baseline" parameter.
94
95 Parameters
96 ----------
97 table : FeatureTable[RelativeFrequency], optional
98 Feature table to optionally use for computing first differences.
99 metadata : Metadata
100 Sample metadata file containing individual_id_column.
101 state_column : Str
102 Metadata column containing state (e.g., Time) across which samples are
103 paired.
104 individual_id_column : Str
105 Metadata column containing IDs for individual subjects.
106 metric : Str
107 Numerical metadata or artifact column to test.
108 replicate_handling : Str % Choices({'drop', 'error', 'random'}), optional
109 Choose how replicate samples are handled. If replicates are detected,
110 "error" causes method to fail; "drop" will discard all replicated
111 samples; "random" chooses one representative at random from among
112 replicates.
113 baseline : Float, optional
114 A value listed in the state_column metadata column against which all
115 other states should be compared. Toggles calculation of static
116 differences instead of first differences (which are calculated if no
117 value is given for baseline). If a "baseline" value is provided, sample
118 differences at each state are compared against the baseline state,
119 instead of the previous state. Must be a value listed in the
120 state_column.
121
122 Returns
123 -------
124 first_differences : SampleData[FirstDifferences]
125 Series of first differences.
126 ]]>
127 </help>
128 <macros>
129 <import>qiime_citation.xml</import>
130 </macros>
131 <expand macro="qiime_citation" />
132 </tool>