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1 <?xml version="1.0" ?>
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2 <tool id="qiime_longitudinal_first-differences" name="qiime longitudinal first-differences" version="2019.4">
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3 <description> - Compute first differences or difference from baseline between sequential states</description>
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4 <requirements>
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5 <requirement type="package" version="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime longitudinal first-differences
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9
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10 --p-state-column="$pstatecolumn"
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6
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11 --p-metric="$pmetric"
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12
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13
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14
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15 #if '__pd__' in str($pindividualidcolumn):
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16 #set $pwhere_temp = $pindividualidcolumn.replace('__pd__', "#")
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17 #set $pindividualidcolumn = $pwhere_temp
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18 #end if
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19 --p-individual-id-column="$pindividualidcolumn"
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6
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20
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21
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0
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22
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23 #if str($itable) != 'None':
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24 --i-table=$itable
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25 #end if
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26
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27 #if str($preplicatehandling) != 'None':
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28 --p-replicate-handling=$preplicatehandling
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29 #end if
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30
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31 #if str($pbaseline):
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32 --p-baseline="$pbaseline"
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33 #end if
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34
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35
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36 #if $input_files_mmetadatafile:
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37 #def list_dict_to_string(list_dict):
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38 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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39 #for d in list_dict[1:]:
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40 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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41 #end for
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42 #return $file_list
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43 #end def
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44 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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45 #end if
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46
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47
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48 --o-first-differences=ofirstdifferences
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49 ;
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50 cp ofirstdifferences.qza $ofirstdifferences
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51 ]]></command>
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52 <inputs>
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53 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text"/>
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54 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text"/>
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55 <param label="--p-metric: TEXT Numerical metadata or artifact column to test. [required]" name="pmetric" optional="False" type="text"/>
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56 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table to optionally use for computing first differences. [optional]" name="itable" optional="True" type="data"/>
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57 <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
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58 <option selected="True" value="None">Selection is Optional</option>
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59 <option value="error">error</option>
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60 <option value="random">random</option>
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61 <option value="drop">drop</option>
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62 </param>
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63 <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 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="float"/>
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64
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65 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]">
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66 <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" />
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67 </repeat>
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68
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69 </inputs>
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70 <outputs>
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71 <data format="qza" label="${tool.name} on ${on_string}: firstdifferences.qza" name="ofirstdifferences"/>
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72 </outputs>
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73 <help><![CDATA[
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74 Compute first differences or difference from baseline between sequential states
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75 ###############################################################################
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76
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77 Calculates first differences in "metric" between sequential states for
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78 samples collected from individual subjects sampled repeatedly at two or
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79 more states. First differences can be performed on a metadata column
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80 (including artifacts that can be input as metadata) or a feature in a
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81 feature table. Outputs a data series of first differences for each
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82 individual subject at each sequential pair of states, labeled by the
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83 SampleID of the second state (e.g., paired differences between time 0 and
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84 time 1 would be labeled by the SampleIDs at time 1). This file can be used
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85 as input to linear mixed effects models or other longitudinal or diversity
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86 methods to compare changes in first differences across time or among groups
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87 of subjects. Also supports differences from baseline (or other static
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88 comparison state) by setting the "baseline" parameter.
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89
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90 Parameters
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91 ----------
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92 metadata : Metadata
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93 Sample metadata file containing individual_id_column.
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94 state_column : Str
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95 Metadata column containing state (time) variable information.
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96 individual_id_column : Str
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97 Metadata column containing IDs for individual subjects.
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98 metric : Str
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99 Numerical metadata or artifact column to test.
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100 replicate_handling : Str % Choices('error', 'random', 'drop'), optional
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101 Choose how replicate samples are handled. If replicates are detected,
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102 "error" causes method to fail; "drop" will discard all replicated
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103 samples; "random" chooses one representative at random from among
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104 replicates.
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105 baseline : Float, optional
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106 A value listed in the state_column metadata column against which all
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107 other states should be compared. Toggles calculation of static
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108 differences instead of first differences (which are calculated if no
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109 value is given for baseline). If a "baseline" value is provided, sample
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110 differences at each state are compared against the baseline state,
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111 instead of the previous state. Must be a value listed in the
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112 state_column.
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113 table : FeatureTable[RelativeFrequency], optional
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114 Feature table to optionally use for computing first differences.
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115
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116 Returns
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117 -------
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118 first_differences : SampleData[FirstDifferences]
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119 Series of first differences.
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120 ]]></help>
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121 <macros>
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122 <import>qiime_citation.xml</import>
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123 </macros>
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124 <expand macro="qiime_citation"/>
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125 </tool>
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