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comparison qiime2/qiime_quality-control_evaluate-composition.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_quality-control_evaluate-composition" name="qiime quality-control evaluate-composition" version="2019.7"> 2 <tool id="qiime_quality-control_evaluate-composition" name="qiime quality-control evaluate-composition"
3 <description> - Evaluate expected vs. observed taxonomic composition of samples</description> 3 version="2020.8">
4 <requirements> 4 <description>Evaluate expected vs. observed taxonomic composition of samples</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime quality-control evaluate-composition 9 qiime quality-control evaluate-composition
9 10
10 --i-expected-features=$iexpectedfeatures 11 --i-expected-features=$iexpectedfeatures
12
11 --i-observed-features=$iobservedfeatures 13 --i-observed-features=$iobservedfeatures
12 14
13 15 --p-depth=$pdepth
14 #if $metadatafile:
15 --m-metadata-file=$metadatafile
16 #end if
17
18
19 #if str($pdepth):
20 --p-depth=$pdepth
21 #end if
22 16
23 #if str($ppalette) != 'None': 17 #if str($ppalette) != 'None':
24 --p-palette=$ppalette 18 --p-palette=$ppalette
25 #end if 19 #end if
26 20
27 #if $pplottar: 21 #if $pnoplottar:
28 --p-plot-tar 22 --p-no-plot-tar
29 #end if 23 #end if
30 24
31 #if $pplottdr: 25 #if $pnoplottdr:
32 --p-plot-tdr 26 --p-no-plot-tdr
33 #end if 27 #end if
34 28
35 #if $pplotrvalue: 29 #if $pplotrvalue:
36 --p-plot-r-value 30 --p-plot-r-value
37 #end if 31 #end if
53 #end if 47 #end if
54 48
55 #if $pnoplotobservedfeaturesratio: 49 #if $pnoplotobservedfeaturesratio:
56 --p-no-plot-observed-features-ratio 50 --p-no-plot-observed-features-ratio
57 #end if 51 #end if
52 # if $input_files_mmetadatafile:
53 # def list_dict_to_string(list_dict):
54 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
55 # for d in list_dict[1:]:
56 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
57 # end for
58 # return $file_list
59 # end def
60 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
61 # end if
62
63 #if '__ob__' in str($mmetadatacolumn):
64 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[')
65 #set $mmetadatacolumn = $mmetadatacolumn_temp
66 #end if
67 #if '__cb__' in str($mmetadatacolumn):
68 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']')
69 #set $mmetadatacolumn = $mmetadatacolumn_temp
70 #end if
71 #if 'X' in str($mmetadatacolumn):
72 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\')
73 #set $mmetadatacolumn = $mmetadatacolumn_temp
74 #end if
75 #if '__sq__' in str($mmetadatacolumn):
76 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
77 #set $mmetadatacolumn = $mmetadatacolumn_temp
78 #end if
79 #if '__db__' in str($mmetadatacolumn):
80 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"')
81 #set $mmetadatacolumn = $mmetadatacolumn_temp
82 #end if
58 83
59 #if str($mmetadatacolumn): 84 #if str($mmetadatacolumn):
60 --m-metadata-column="$mmetadatacolumn" 85 --m-metadata-column=$mmetadatacolumn
61 #end if 86 #end if
62 87
63 --o-visualization=ovisualization 88 --o-visualization=ovisualization
89
90 #if str($examples) != 'None':
91 --examples=$examples
92 #end if
93
64 ; 94 ;
65 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 95 cp odatabase.qza $odatabase
96
97 ;
98 qiime tools export ovisualization.qzv --output-path out
99 && mkdir -p '$ovisualization.files_path'
66 && cp -r out/* '$ovisualization.files_path' 100 && cp -r out/* '$ovisualization.files_path'
67 && mv '$ovisualization.files_path/index.html' '$ovisualization' 101 && mv '$ovisualization.files_path/index.html' '$ovisualization'
68 ]]></command> 102
69 <inputs> 103 ]]></command>
70 <param format="qza,no_unzip.zip" label="--i-expected-features: ARTIFACT FeatureTable[RelativeFrequency] Expected feature compositions [required]" name="iexpectedfeatures" optional="False" type="data"/> 104 <inputs>
71 <param format="qza,no_unzip.zip" label="--i-observed-features: ARTIFACT FeatureTable[RelativeFrequency] Observed feature compositions [required]" name="iobservedfeatures" optional="False" type="data"/> 105 <param format="qza,no_unzip.zip" label="--i-expected-features: ARTIFACT FeatureTable[RelativeFrequency] Expected feature compositions [required]" name="iexpectedfeatures" optional="False" type="data" />
72 <param label="--p-depth: INTEGER Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 = root, 7 = species for the greengenes reference sequence database). [default: 7]" name="pdepth" optional="True" type="integer" value="7"/> 106 <param format="qza,no_unzip.zip" label="--i-observed-features: ARTIFACT FeatureTable[RelativeFrequency] Observed feature compositions [required]" name="iobservedfeatures" optional="False" type="data" />
73 <param label="--p-palette: " name="ppalette" optional="True" type="select"> 107 <param label="--p-depth: INTEGER Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 = root, 7 = species for the greengenes reference sequence database). [default: 7]" name="pdepth" optional="True" type="integer" value="7" />
74 <option selected="True" value="None">Selection is Optional</option> 108 <param label="--p-palette: " name="ppalette" optional="True" type="select">
75 <option value="Set1">Set1</option> 109 <option selected="True" value="None">Selection is Optional</option>
76 <option value="Set2">Set2</option> 110 <option value="Set1">Set1</option>
77 <option value="Set3">Set3</option> 111 <option value="Set2">Set2</option>
78 <option value="Pastel1">Pastel1</option> 112 <option value="Set3">Set3</option>
79 <option value="Pastel2">Pastel2</option> 113 <option value="Pastel1">Pastel1</option>
80 <option value="Paired">Paired</option> 114 <option value="Pastel2">Pastel2</option>
81 <option value="Accent">Accent</option> 115 <option value="Paired">Paired</option>
82 <option value="Dark2">Dark2</option> 116 <option value="Accent">Accent</option>
83 <option value="tab10">tab10</option> 117 <option value="Dark2">Dark2</option>
84 <option value="tab20">tab20</option> 118 <option value="tab10">tab10</option>
85 <option value="tab20b">tab20b</option> 119 <option value="tab20">tab20</option>
86 <option value="tab20c">tab20c</option> 120 <option value="tab20b">tab20b</option>
87 <option value="viridis">viridis</option> 121 <option value="tab20c">tab20c</option>
88 <option value="plasma">plasma</option> 122 <option value="viridis">viridis</option>
89 <option value="inferno">inferno</option> 123 <option value="plasma">plasma</option>
90 <option value="magma">magma</option> 124 <option value="inferno">inferno</option>
91 <option value="terrain">terrain</option> 125 <option value="magma">magma</option>
92 <option value="rainbow">rainbow</option> 126 <option value="terrain">terrain</option>
93 </param> 127 <option value="rainbow">rainbow</option>
94 <param label="--p-plot-tar: --p-no-plot-tar Plot taxon accuracy rate (TAR) on score plot. TAR is the number of true positive features divided by the total number of observed features (TAR = true positives " name="pplottar" selected="False" type="boolean"/> 128 </param>
95 <param label="--p-plot-tdr: --p-no-plot-tdr Plot taxon detection rate (TDR) on score plot. TDR is the number of true positive features divided by the total number of expected features (TDR = true positives " name="pplottdr" selected="False" type="boolean"/> 129 <param label="--p-no-plot-tar: Do not plot taxon accuracy rate (TAR) on score plot. TAR is the number of true positive features divided by the total number of observed features (TAR = true positives / (true positives + false positives)). [default: True]" name="pnoplottar" selected="False" type="boolean" />
96 <param label="--p-plot-r-value: --p-no-plot-r-value Plot expected vs. observed linear regression r value on score plot. [default: False]" name="pplotrvalue" selected="False" type="boolean"/> 130 <param label="--p-no-plot-tdr: Do not plot taxon detection rate (TDR) on score plot. TDR is the number of true positive features divided by the total number of expected features (TDR = true positives / (true positives + false negatives)). [default: True]" name="pnoplottdr" selected="False" type="boolean" />
97 <param label="--p-no-plot-r-squared: Do not plot expected vs. observed linear regression r-squared value on score plot. [default: False]" name="pnoplotrsquared" selected="False" type="boolean"/> 131 <param label="--p-plot-r-value: --p-plot-r-value: / --p-no-plot-r-value Plot expected vs. observed linear regression r value on score plot. [default: False]" name="pplotrvalue" selected="False" type="boolean" />
98 <param label="--p-plot-bray-curtis: --p-no-plot-bray-curtis Plot expected vs. observed Bray-Curtis dissimilarity scores on score plot. [default: False]" name="pplotbraycurtis" selected="False" type="boolean"/> 132 <param label="--p-no-plot-r-squared: Do not plot expected vs. observed linear regression r-squared value on score plot. [default: True]" name="pnoplotrsquared" selected="False" type="boolean" />
99 <param label="--p-plot-jaccard: --p-no-plot-jaccard Plot expected vs. observed Jaccard distances scores on score plot. [default: False]" name="pplotjaccard" selected="False" type="boolean"/> 133 <param label="--p-plot-bray-curtis: --p-plot-bray-curtis: / --p-no-plot-bray-curtis Plot expected vs. observed Bray-Curtis dissimilarity scores on score plot. [default: False]" name="pplotbraycurtis" selected="False" type="boolean" />
100 <param label="--p-plot-observed-features: --p-no-plot-observed-features Plot observed features count on score plot. [default: False]" name="pplotobservedfeatures" selected="False" type="boolean"/> 134 <param label="--p-plot-jaccard: --p-plot-jaccard: / --p-no-plot-jaccard Plot expected vs. observed Jaccard distances scores on score plot. [default: False]" name="pplotjaccard" selected="False" type="boolean" />
101 <param label="--p-no-plot-observed-features-ratio: Do not plot ratio of observed:expected features on score plot. [default: False]" name="pnoplotobservedfeaturesratio" selected="False" type="boolean"/> 135 <param label="--p-plot-observed-features: --p-plot-observed-features: / --p-no-plot-observed-features Plot observed features count on score plot. [default: False]" name="pplotobservedfeatures" selected="False" type="boolean" />
102 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Optional sample metadata that maps observed-features sample IDs to expected-features sample IDs. [optional]" name="mmetadatacolumn" optional="True" type="text"/> 136 <param label="--p-no-plot-observed-features-ratio: Do not plot ratio of observed:expected features on score plot. [default: True]" name="pnoplotobservedfeaturesratio" selected="False" type="boolean" />
103 137 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
104 <param label="--m-metadata-file METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" /> 138 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
105 139 </repeat>
106 140 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Optional sample metadata that maps observed-features sample IDs to expected-features sample IDs. [optional]" name="mmetadatacolumn" optional="False" type="text" />
107 </inputs> 141 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
108 <outputs> 142
109 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 143 </inputs>
110 </outputs> 144
111 <help><![CDATA[ 145 <outputs>
146 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
147
148 </outputs>
149
150 <help><![CDATA[
112 Evaluate expected vs. observed taxonomic composition of samples 151 Evaluate expected vs. observed taxonomic composition of samples
113 ############################################################### 152 ###############################################################
114 153
115 This visualizer compares the feature composition of pairs of observed and 154 This visualizer compares the feature composition of pairs of observed and
116 expected samples containing the same sample ID in two separate feature 155 expected samples containing the same sample ID in two separate feature
165 expected_features sample IDs. 204 expected_features sample IDs.
166 205
167 Returns 206 Returns
168 ------- 207 -------
169 visualization : Visualization 208 visualization : Visualization
170 ]]></help> 209 ]]></help>
171 <macros> 210 <macros>
172 <import>qiime_citation.xml</import> 211 <import>qiime_citation.xml</import>
173 </macros> 212 </macros>
174 <expand macro="qiime_citation"/> 213 <expand macro="qiime_citation"/>
175 </tool> 214 </tool>