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1 <?xml version="1.0" ?>
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2 <tool id="qiime_gneiss_dendrogram-heatmap" name="qiime gneiss dendrogram-heatmap" version="2019.4">
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3 <description> - Dendrogram heatmap.</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 gneiss dendrogram-heatmap
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9
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10 --i-table=$itable
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11 --i-tree=$itree
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12 --m-metadata-column="$mmetadatacolumn"
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13
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14
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15 #if $input_files_mmetadatafile:
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16 #def list_dict_to_string(list_dict):
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17 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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18 #for d in list_dict[1:]:
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19 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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20 #end for
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21 #return $file_list
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22 #end def
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23 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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24 #end if
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25
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26
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6
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27 #if str($ppseudocount):
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0
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28 --p-pseudocount=$ppseudocount
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29 #end if
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30
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6
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31 #if str($pndim):
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0
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32 --p-ndim=$pndim
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33 #end if
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34
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35 #if str($pmethod) != 'None':
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36 --p-method=$pmethod
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37 #end if
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38
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39 #if str($pcolormap) != 'None':
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40 --p-color-map=$pcolormap
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41 #end if
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42
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43 --o-visualization=ovisualization
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44 ;
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45 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
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46 && cp -r out/* '$ovisualization.files_path'
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47 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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48 ]]></command>
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49 <inputs>
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50 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table that will be plotted as a heatmap. This table is assumed to have strictly positive values. [required]" name="itable" optional="False" type="data"/>
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51 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT A hierarchy of feature identifiers where each Hierarchy tipcorresponds to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="itree" optional="False" type="data"/>
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52 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Categorical metadata column to group the samples. [required]" name="mmetadatacolumn" optional="False" type="text"/>
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53 <param label="--p-pseudocount: NUMBER The pseudocount to add to avoid division by zero. [default: 0.5]" name="ppseudocount" optional="True" type="float" value="0.5"/>
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54 <param label="--p-ndim: INTEGER Number of dimensions to highlight. [default: 10]" name="pndim" optional="True" type="integer" value="10"/>
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55 <param label="--p-method: " name="pmethod" optional="True" type="select">
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56 <option selected="True" value="None">Selection is Optional</option>
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57 <option value="clr">clr</option>
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58 <option value="log">log</option>
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59 </param>
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60 <param label="--p-color-map: " name="pcolormap" optional="True" type="select">
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61 <option selected="True" value="None">Selection is Optional</option>
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62 <option value="viridis">viridis</option>
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63 <option value="inferno">inferno</option>
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64 <option value="plasma">plasma</option>
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65 <option value="magma">magma</option>
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66 <option value="Blues">Blues</option>
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67 <option value="BuGn">BuGn</option>
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68 <option value="BuPu">BuPu</option>
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69 <option value="GnBu">GnBu</option>
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70 <option value="Greens">Greens</option>
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71 <option value="Greys">Greys</option>
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72 <option value="Oranges">Oranges</option>
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73 <option value="OrRd">OrRd</option>
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74 <option value="PuBu">PuBu</option>
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75 <option value="PuBuGn">PuBuGn</option>
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76 <option value="PuRd">PuRd</option>
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77 <option value="Purples">Purples</option>
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78 <option value="RdPu">RdPu</option>
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79 <option value="Reds">Reds</option>
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80 <option value="YlGn">YlGn</option>
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81 <option value="YlGnBu">YlGnBu</option>
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82 <option value="YlOrBr">YlOrBr</option>
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83 <option value="YlOrRd">YlOrRd</option>
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84 <option value="afmhot">afmhot</option>
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85 <option value="autumn">autumn</option>
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86 <option value="bone">bone</option>
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87 <option value="cool">cool</option>
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88 <option value="copper">copper</option>
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89 <option value="gist_heat">gist_heat</option>
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90 <option value="gray">gray</option>
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91 <option value="hot">hot</option>
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92 <option value="pink">pink</option>
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93 <option value="spring">spring</option>
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94 <option value="summer">summer</option>
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95 <option value="winter">winter</option>
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96 <option value="BrBG">BrBG</option>
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97 <option value="bwr">bwr</option>
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98 <option value="coolwarm">coolwarm</option>
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99 <option value="PiYG">PiYG</option>
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100 <option value="PRGn">PRGn</option>
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101 <option value="PuOr">PuOr</option>
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102 <option value="RdBu">RdBu</option>
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103 <option value="RdGy">RdGy</option>
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104 <option value="RdYlBu">RdYlBu</option>
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105 <option value="RdYlGn">RdYlGn</option>
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106 <option value="Spectral">Spectral</option>
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107 <option value="seismic">seismic</option>
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108 <option value="Accent">Accent</option>
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109 <option value="Dark2">Dark2</option>
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110 <option value="Paired">Paired</option>
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111 <option value="Pastel1">Pastel1</option>
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112 <option value="Pastel2">Pastel2</option>
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113 <option value="Set1">Set1</option>
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114 <option value="Set2">Set2</option>
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115 <option value="Set3">Set3</option>
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116 <option value="Vega10">Vega10</option>
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117 <option value="Vega20">Vega20</option>
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118 <option value="Vega20b">Vega20b</option>
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119 <option value="Vega20c">Vega20c</option>
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120 <option value="gist_earth">gist_earth</option>
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121 <option value="terrain">terrain</option>
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122 <option value="ocean">ocean</option>
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123 <option value="gist_stern">gist_stern</option>
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124 <option value="brg">brg</option>
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125 <option value="CMRmap">CMRmap</option>
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126 <option value="cubehelix">cubehelix</option>
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127 <option value="gnuplot">gnuplot</option>
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128 <option value="gnuplot2">gnuplot2</option>
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129 <option value="gist_ncar">gist_ncar</option>
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130 <option value="nipy_spectral">nipy_spectral</option>
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131 <option value="jet">jet</option>
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132 <option value="rainbow">rainbow</option>
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133 <option value="gist_rainbow">gist_rainbow</option>
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134 <option value="hsv">hsv</option>
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135 <option value="flag">flag</option>
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136 <option value="prism">prism</option>
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137 </param>
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138
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139 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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140 <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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141 </repeat>
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142
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143 </inputs>
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144 <outputs>
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145 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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146 </outputs>
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147 <help><![CDATA[
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148 Dendrogram heatmap.
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149 ###################
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150
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151 Visualize the feature table as a heatmap, with samples sorted along a
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152 specified categorical metadata column and features clustered together
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153 specified by the tree.
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154
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155 Parameters
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156 ----------
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157 table : FeatureTable[Frequency]
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158 The feature table that will be plotted as a heatmap. This table is
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159 assumed to have strictly positive values.
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160 tree : Hierarchy
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161 A hierarchy of feature identifiers where each tipcorresponds to the
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162 feature identifiers in the table. This tree can contain tip ids that
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163 are not present in the table, but all feature ids in the table must be
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164 present in this tree.
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165 metadata : MetadataColumn[Categorical]
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166 Categorical metadata column to group the samples.
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167 pseudocount : Float, optional
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168 The pseudocount to add to avoid division by zero.
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169 ndim : Int, optional
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170 Number of dimensions to highlight.
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171 method : Str % Choices('clr', 'log'), optional
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172 Specifies how the data should be normalized for display.Options include
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173 'log' or 'clr' (default='clr').
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174 color_map : Str % Choices('viridis', 'inferno', 'plasma', 'magma', 'Blues', 'BuGn', 'BuPu', 'GnBu', 'Greens', 'Greys', 'Oranges', 'OrRd', 'PuBu', 'PuBuGn', 'PuRd', 'Purples', 'RdPu', 'Reds', 'YlGn', 'YlGnBu', 'YlOrBr', 'YlOrRd', 'afmhot', 'autumn', 'bone', 'cool', 'copper', 'gist_heat', 'gray', 'hot', 'pink', 'spring', 'summer', 'winter', 'BrBG', 'bwr', 'coolwarm', 'PiYG', 'PRGn', 'PuOr', 'RdBu', 'RdGy', 'RdYlBu', 'RdYlGn', 'Spectral', 'seismic', 'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2', 'Set1', 'Set2', 'Set3', 'Vega10', 'Vega20', 'Vega20b', 'Vega20c', 'gist_earth', 'terrain', 'ocean', 'gist_stern', 'brg', 'CMRmap', 'cubehelix', 'gnuplot', 'gnuplot2', 'gist_ncar', 'nipy_spectral', 'jet', 'rainbow', 'gist_rainbow', 'hsv', 'flag', 'prism'), optional
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175 Specifies the color map for plotting the heatmap. See
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176 https://matplotlib.org/examples/color/colormaps_reference.html for more
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177 details.
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178
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179 Returns
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180 -------
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181 visualization : Visualization
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182 ]]></help>
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183 <macros>
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184 <import>qiime_citation.xml</import>
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185 </macros>
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186 <expand macro="qiime_citation"/>
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187 </tool>
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