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annotate make_otu_heatmap.xml @ 0:c1bd0c560018 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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1 <tool id="qiime_make_otu_heatmap" name="make otu heatmap" version="1.9.1galaxy1">
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2 <description>Plot heatmap of OTU table</description>
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3
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7
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8 <expand macro="requirements" />
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9
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10 <command>
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11 <![CDATA[
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12 make_otu_heatmap.py
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13 -i $otu_table_fp
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14 -o make_otu_heatmap_output
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15
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16 #if str($otu_tree) != 'None':
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17 -t $otu_tree
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18 #end if
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19
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20 #if str($map_fname) != 'None':
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21 -m $map_fname
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22 #end if
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24 #if str($category):
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25 -c $category
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26 #end if
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27
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28 #if str($sample_tree) != 'None':
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29 -s $sample_tree
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30 #end if
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31
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32 #if $no_log_transform:
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33 --no_log_transform
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34 #end if
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35
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36 #if $suppress_row_clustering:
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37 --suppress_row_clustering
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38 #end if
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39
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40 #if $suppress_column_clustering:
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41 --suppress_column_clustering
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42 #end if
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43
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44 #if $absolute_abundance:
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45 --absolute_abundance
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46 #end if
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47
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48 #if str($ad.select) == "yes":
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49 #if $ad.color_scheme:
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50 --color_scheme $ad.color_scheme
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51 #end if
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52
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53 #if $ad.width:
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54 --width $ad.width
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55 #end if
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56
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57 #if $ad.height:
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58 --height $ad.height
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59 #end if
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60
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61 #if $ad.dpi:
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62 --dpi $ad.dpi
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63 #end if
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64
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65 #if $ad.obs_md_category:
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66 --obs_md_category $ad.obs_md_category
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67 #end if
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68
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69 #if $ad.obs_md_level:
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70 --obs_md_level $ad.obs_md_level
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71 #end if
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72 #end if
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73 ]]>
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74
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75 </command>
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76
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77 <inputs>
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78 <param label="-i/--otu_table_fp: path to the input OTU table (i.e., the
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79 output from make_otu_table.py)" name="otu_table_fp" optional="False"
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80 type="data"/>
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81 <param default="None" label="-t/--otu_tree: Tree file to be used for
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82 sorting OTUs in the heatmap" name="otu_tree" optional="True"
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83 type="data"/>
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84 <param default="None" label="-m/--map_fname: Metadata mapping file to be
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85 used for sorting Samples in the heatmap." name="map_fname" optional="True"
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86 type="data"/>
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87 <param default="None" label="-c/--category: Metadata category for sorting
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88 samples. Samples will be clustered within each category level using
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89 euclidean UPGMA." name="category" optional="True" type="text"/>
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90 <param default="None" label="-s/--sample_tree: Tree file to be used for
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91 sorting samples (e.g, output from upgma_cluster.py). If both this and
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92 the sample mapping file are provided, the mapping file is ignored."
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93 name="sample_tree" optional="True" type="data"/>
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94 <param label="--no_log_transform: Data will not be log-transformed. Without
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95 this option, all zeros will be set to a small value (default is 1/2
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96 the smallest non-zero entry). Data will be translated to be non-negative
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97 after log transform, and num_otu_hits will be set to 0."
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98 name="no_log_transform" selected="False" type="boolean"/>
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99 <param label="--suppress_row_clustering: No UPGMA clustering of OTUs (rows)
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100 is performed. If --otu_tree is provided, this flag is ignored."
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101 name="suppress_row_clustering" selected="False" type="boolean"/>
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102 <param label="--suppress_column_clustering: No UPGMA clustering of Samples
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103 (columns) is performed. If --map_fname is provided, this flag is ignored."
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104 name="suppress_column_clustering" selected="False" type="boolean"/>
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105 <param label="--absolute_abundance: Do not normalize samples to sum to 1.
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106 [default False]" name="absolute_abundance" selected="False"
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107 type="boolean"/>
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108
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109 <conditional name="ad">
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110 <param name="select" type="select" label="Show advanced options">
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111 <option value="no" selected="True">No</option>
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112 <option value="yes">Yes</option>
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113 </param>
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114 <when value="no">
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115 </when>
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116 <when value="yes">
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117 <param default="YlGn" label="Color scheme for figure. see http://matplotlib.org/examples/color/colormaps_reference.html for choices [default: YlGn]"
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118 name="color_scheme" optional="True" type="text"/>
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119 <param default="5" label="Width of the figure in inches [default: 5]"
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120 name="width" optional="True" type="text"/>
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121 <param default="5" label="Height of the figure in inches [default: 5]"
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122 name="height" optional="True" type="text"/>
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123 <param label="Resolution of the figure in dots per inch [default:
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124 value of savefig.dpi in matplotlibrc file]" name="dpi"
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125 optional="True" type="text"/>
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126 <param label="Observation metadata category to plot [default: taxonomy]"
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127 name="obs_md_category" optional="True" type="data"/>
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128 <param label="The level of observation metadata to plot for hierarchical
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129 metadata [default: lowest level]" name="obs_md_level" optional="True"
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130 type="data"/>
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131 </when>
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132 </conditional>
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133 </inputs>
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134
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135 <outputs>
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136 <data format="pdf" from_work_dir="make_otu_heatmap_output" name="heatmap_OTU"
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137 label="heatmap_OTU.pdf"/>
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138 </outputs>
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139
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140 <tests>
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141 <test>
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142 </test>
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143 </tests>
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144
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145 <help><![CDATA[
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146
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147 **What it does**
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148
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149 This script visualizes an OTU table as a heatmap where each row corresponds to an
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150 OTU and each column corresponds to a sample. The higher the relative abundance of
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151 an OTU in a sample, the more intense the color at the corresponsing position in
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152 the heatmap. By default, the OTUs (rows) will be clustered by UPGMA hierarchical
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153 clustering, and the samples (columns) will be presented in the order in which
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154 they appear in the OTU table. Alternatively, the user may supply a tree to sort
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155 the OTUs (rows) or samples (columns), or both. The user may also pass in a mapping
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156 file for sorting samples. If the user passes in a mapping file and a metadata
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157 category, samples (columns) will be grouped by category value and subsequently
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158 clustered within each group.
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159 A single output file is created containing the heatmap of the OTU table (a PDF
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160 file by default).
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161 ]]>
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162 </help>
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163
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164 <citations>
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165 <expand macro="citations" />
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166 </citations>
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167 </tool>