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1 <?xml version="1.0" ?>
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2 <tool id="qiime_composition_ancom" name="qiime composition ancom"
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3 version="2020.8">
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4 <description>Apply ANCOM to identify features that differ in abundance.</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 composition ancom
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10
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11 --i-table=$itable
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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($input_files_mmetadatafile)
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21 # end if
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22
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23 #if '__ob__' in str($mmetadatacolumn):
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24 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[')
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25 #set $mmetadatacolumn = $mmetadatacolumn_temp
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26 #end if
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27 #if '__cb__' in str($mmetadatacolumn):
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28 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']')
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29 #set $mmetadatacolumn = $mmetadatacolumn_temp
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30 #end if
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31 #if 'X' in str($mmetadatacolumn):
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32 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\')
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33 #set $mmetadatacolumn = $mmetadatacolumn_temp
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34 #end if
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35 #if '__sq__' in str($mmetadatacolumn):
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36 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
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37 #set $mmetadatacolumn = $mmetadatacolumn_temp
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38 #end if
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39 #if '__db__' in str($mmetadatacolumn):
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40 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"')
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41 #set $mmetadatacolumn = $mmetadatacolumn_temp
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42 #end if
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43
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44 --m-metadata-column=$mmetadatacolumn
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45
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46
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47 #if str($ptransformfunction) != 'None':
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48 --p-transform-function=$ptransformfunction
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49 #end if
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50
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51 #if str($pdifferencefunction) != 'None':
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52 --p-difference-function=$pdifferencefunction
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53 #end if
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54
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55 --o-visualization=ovisualization
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56
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57 #if str($examples) != 'None':
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58 --examples=$examples
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59 #end if
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60
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61 ;
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62 cp ocompositiontable.qza $ocompositiontable
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63
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64 ;
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65 qiime tools export ovisualization.qzv --output-path out
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66 && mkdir -p '$ovisualization.files_path'
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67 && cp -r out/* '$ovisualization.files_path'
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68 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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69
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70 ]]></command>
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71 <inputs>
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72 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Composition] The feature table to be used for ANCOM computation. [required]" name="itable" optional="False" type="data" />
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73 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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74 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
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75 </repeat>
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76 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] The categorical sample metadata column to test for differential abundance across. [required]" name="mmetadatacolumn" optional="False" type="text" />
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77 <param label="--p-transform-function: " name="ptransformfunction" optional="True" type="select">
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78 <option selected="True" value="None">Selection is Optional</option>
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79 <option value="sqrt">sqrt</option>
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80 <option value="log">log</option>
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81 <option value="clr">clr</option>
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82 </param>
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83 <param label="--p-difference-function: " name="pdifferencefunction" optional="True" type="select">
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84 <option selected="True" value="None">Selection is Optional</option>
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85 <option value="mean_difference">mean_difference</option>
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86 <option value="f_statistic">f_statistic</option>
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87 </param>
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88 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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89
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90 </inputs>
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91
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92 <outputs>
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93 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
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94
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95 </outputs>
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96
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97 <help><![CDATA[
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98 Apply ANCOM to identify features that differ in abundance.
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99 ###############################################################
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100
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101 Apply Analysis of Composition of Microbiomes (ANCOM) to identify features
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102 that are differentially abundant across groups.
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103
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104 Parameters
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105 ----------
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106 table : FeatureTable[Composition]
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107 The feature table to be used for ANCOM computation.
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108 metadata : MetadataColumn[Categorical]
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109 The categorical sample metadata column to test for differential
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110 abundance across.
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111 transform_function : Str % Choices('sqrt', 'log', 'clr'), optional
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112 The method applied to transform feature values before generating
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113 volcano plots.
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114 difference_function : Str % Choices('mean_difference', 'f_statistic'), optional
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115 The method applied to visualize fold difference in feature abundances
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116 across groups for volcano plots.
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117
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118 Returns
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119 -------
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120 visualization : Visualization
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121 ]]></help>
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122 <macros>
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123 <import>qiime_citation.xml</import>
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124 </macros>
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125 <expand macro="qiime_citation"/>
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126 </tool> |
