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1 <?xml version="1.0" ?>
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2 <tool id="qiime_longitudinal_first-distances" name="qiime longitudinal first-distances"
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3 version="2020.8">
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4 <description>Compute first distances or distance from baseline between sequential states</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime longitudinal first-distances
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10
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11 --i-distance-matrix=$idistancematrix
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12 # if $input_files_mmetadatafile:
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13 # def list_dict_to_string(list_dict):
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14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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15 # for d in list_dict[1:]:
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16 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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17 # end for
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18 # return $file_list
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19 # end def
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20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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21 # end if
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22
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23 #if '__ob__' in str($pstatecolumn):
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24 #set $pstatecolumn_temp = $pstatecolumn.replace('__ob__', '[')
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25 #set $pstatecolumn = $pstatecolumn_temp
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26 #end if
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27 #if '__cb__' in str($pstatecolumn):
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28 #set $pstatecolumn_temp = $pstatecolumn.replace('__cb__', ']')
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29 #set $pstatecolumn = $pstatecolumn_temp
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30 #end if
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31 #if 'X' in str($pstatecolumn):
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32 #set $pstatecolumn_temp = $pstatecolumn.replace('X', '\\')
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33 #set $pstatecolumn = $pstatecolumn_temp
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34 #end if
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35 #if '__sq__' in str($pstatecolumn):
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36 #set $pstatecolumn_temp = $pstatecolumn.replace('__sq__', "'")
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37 #set $pstatecolumn = $pstatecolumn_temp
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38 #end if
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39 #if '__db__' in str($pstatecolumn):
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40 #set $pstatecolumn_temp = $pstatecolumn.replace('__db__', '"')
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41 #set $pstatecolumn = $pstatecolumn_temp
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42 #end if
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43
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44 --p-state-column=$pstatecolumn
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45
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46
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47 #if '__ob__' in str($pindividualidcolumn):
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48 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
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49 #set $pindividualidcolumn = $pindividualidcolumn_temp
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50 #end if
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51 #if '__cb__' in str($pindividualidcolumn):
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52 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
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53 #set $pindividualidcolumn = $pindividualidcolumn_temp
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54 #end if
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55 #if 'X' in str($pindividualidcolumn):
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56 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
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57 #set $pindividualidcolumn = $pindividualidcolumn_temp
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58 #end if
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59 #if '__sq__' in str($pindividualidcolumn):
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60 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
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61 #set $pindividualidcolumn = $pindividualidcolumn_temp
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62 #end if
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63 #if '__db__' in str($pindividualidcolumn):
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64 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
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65 #set $pindividualidcolumn = $pindividualidcolumn_temp
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66 #end if
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67
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68 --p-individual-id-column=$pindividualidcolumn
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69
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70
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71 #if str($pbaseline):
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72 --p-baseline=$pbaseline
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73 #end if
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74 #if str($preplicatehandling) != 'None':
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75 --p-replicate-handling=$preplicatehandling
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76 #end if
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77
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78 --o-first-distances=ofirstdistances
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79
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80 #if str($examples) != 'None':
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81 --examples=$examples
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82 #end if
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83
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84 ;
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85 cp ofirstdistances.qza $ofirstdistances
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86
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87 ]]></command>
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88 <inputs>
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89 <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" />
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90 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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91 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata file containing arguments will be individual-id-column. merged) [required]" name="additional_input" optional="False" type="data" />
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92 </repeat>
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93 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text" />
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94 <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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95 <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="False" type="text" />
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96 <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
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97 <option selected="True" value="None">Selection is Optional</option>
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98 <option value="error">error</option>
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99 <option value="random">random</option>
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100 <option value="drop">drop</option>
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101 </param>
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102 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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103
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104 </inputs>
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105
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106 <outputs>
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107 <data format="qza" label="${tool.name} on ${on_string}: firstdistances.qza" name="ofirstdistances" />
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108
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109 </outputs>
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110
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111 <help><![CDATA[
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112 Compute first distances or distance from baseline between sequential states
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113 ###############################################################
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114
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115 Calculates first distances between sequential states for samples collected
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116 from individual subjects sampled repeatedly at two or more states. This
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117 method is similar to the "first differences" method, except that it
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118 requires a distance matrix as input and calculates first differences as
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119 distances between successive states. Outputs a data series of first
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120 distances for each individual subject at each sequential pair of states,
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121 labeled by the SampleID of the second state (e.g., paired distances between
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122 time 0 and time 1 would be labeled by the SampleIDs at time 1). This file
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123 can be used as input to linear mixed effects models or other longitudinal
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124 or diversity methods to compare changes in first distances across time or
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125 among groups of subjects. Also supports distance from baseline (or other
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126 static comparison state) by setting the "baseline" parameter.
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127
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128 Parameters
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129 ----------
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130 distance_matrix : DistanceMatrix
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131 Matrix of distances between pairs of samples.
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132 metadata : Metadata
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133 Sample metadata file containing individual_id_column.
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134 state_column : Str
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135 Metadata column containing state (time) variable information.
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136 individual_id_column : Str
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137 Metadata column containing IDs for individual subjects.
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138 baseline : Float, optional
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139 A value listed in the state_column metadata column against which all
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140 other states should be compared. Toggles calculation of static
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141 distances instead of first distances (which are calculated if no value
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142 is given for baseline). If a "baseline" value is provided, sample
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143 distances at each state are compared against the baseline state,
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144 instead of the previous state. Must be a value listed in the
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145 state_column.
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146 replicate_handling : Str % Choices('error', 'random', 'drop'), optional
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147 Choose how replicate samples are handled. If replicates are detected,
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148 "error" causes method to fail; "drop" will discard all replicated
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149 samples; "random" chooses one representative at random from among
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150 replicates.
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151
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152 Returns
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153 -------
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154 first_distances : SampleData[FirstDifferences]
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155 Series of first distances.
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156 ]]></help>
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157 <macros>
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158 <import>qiime_citation.xml</import>
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159 </macros>
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160 <expand macro="qiime_citation"/>
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161 </tool> |
