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