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annotate plot_taxa_summary.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_plot_taxa_summary" name="Make taxonomy summary charts" version="1.9.1">
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2 <description>based on taxonomy assignment</description>
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3
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4 <macros>
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5 <import>macros.xml</import>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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6 </macros>
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8 <expand macro="requirements" />
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10 <version_command><![CDATA[
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11 plot_taxa_summary.py --version
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12 ]]>
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13 </version_command>
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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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15 <command>
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16 <![CDATA[
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17 #set $chosen_chart_type = str( $chart_type ).split( "," )
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19 plot_taxa_summary.py
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20 -i $counts_fname
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21
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22 -o taxa_plots
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23
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24 #if str($labels):
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25 -l $labels
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26 #end if
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27
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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28 -n $num_categories
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29
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30 #if str( $colorby)
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31 -b $colorby
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32 #end if
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33
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34 -k $background_color
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35 -d $dpi
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36 -x $x_width
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37 -y $y_height
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38 -w $bar_width
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39
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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40 -c $chart_type
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41 $include_html_legend
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42 -a $label_type
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43
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44 #if "area" in $chosen_chart_type:
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45 &&
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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46 mkdir -p $area_charts_html_report.files_path
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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47 &&
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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48 cp -r taxa_plots/area_charts.html $area_charts_html_report.files_path
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49 &&
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50 cp -r taxa_plots/charts $area_charts_html_report.files_path
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51 &&
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52 cp -r taxa_plots/css $area_charts_html_report.files_path
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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53 &&
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54 cp -r taxa_plots/js $area_charts_html_report.files_path
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55 &&
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56 mv $area_charts_html_report.files_path/area_charts.html $area_charts_html_report
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57 #end if
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58
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59 #if "bar" in $chosen_chart_type:
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60 &&
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61 mkdir -p $bar_charts_html_report.files_path
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62 &&
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63 cp -r taxa_plots/bar_charts.html $bar_charts_html_report.files_path
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64 &&
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65 cp -r taxa_plots/charts $bar_charts_html_report.files_path
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66 &&
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67 cp -r taxa_plots/css $bar_charts_html_report.files_path
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68 &&
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69 cp -r taxa_plots/js $bar_charts_html_report.files_path
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70 &&
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71 mv $bar_charts_html_report.files_path/bar_charts.html $bar_charts_html_report
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72 #end if
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73
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74 #if "pie" in $chosen_chart_type:
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75 &&
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76 mkdir -p $pie_charts_html_report.files_path
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77 &&
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78 cp -r taxa_plots/pie_charts.html $pie_charts_html_report.files_path
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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79 &&
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80 cp -r taxa_plots/charts $pie_charts_html_report.files_path
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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81 &&
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82 cp -r taxa_plots/css $pie_charts_html_report.files_path
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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83 &&
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84 cp -r taxa_plots/js $pie_charts_html_report.files_path
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85 &&
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86 mv $pie_charts_html_report.files_path/pie_charts.html $pie_charts_html_report
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87 #end if
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88 ]]>
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89 </command>
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90
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diff changeset
91 <inputs>
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92 <param name="counts_fname" type="data" format="tabular,txt,tsv"
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93 label="Summarized taxa files" multiple="True"
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94 help="(-i/--counts_fname)"/>
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95
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96 <param name="labels" type="text" value="" label="Comma-separated list of
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97 taxonomic levels (optional)" help="(-l/--labels)" optional="True"/>
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98
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99 <param name="num_categories" type="integer" value="20" label="Maximum
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100 number of taxonomies to show in each pie chart" help="All additional
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101 taxonomies are grouped into an 'other' category. This functionality
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102 only applies to the pie charts(-n/--num_categories)"/>
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103
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104 <param name="colorby" type="text" value="" label="Categories to color
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105 by in the plots from the metadata mapping file (optional)"
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106 help="The categories must match the name of a column header in the
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107 mapping file exactly and multiple categories can be list by comma
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108 separating them without spaces(-b/--colorby)" optional="True"/>
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109
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110 <param name="background_color" type="select" label="Background color to
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111 use in the plots" help="(-k/--background_color)">
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112 <option value="white">White</option>
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113 <option value="black">Black</option>
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114 </param>
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115
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116 <param name="dpi" type="integer" value="80" label="Resolution of the plot"
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117 help="(-d/--dpi)"/>
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118
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119 <param name="x_width" type="integer" value="12" label="Width of the
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120 x-axis to use in the plots" help="(-x/--x_width)"/>
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121
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122 <param name="y_height" type="integer" value="12" label="Height of the
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123 y-axis to use in the plots" help="(-y/--y_height)"/>
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124
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125 <param name="bar_width" type="float" value="0.75" min="0" maw="1"
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126 label="Width of the bars in the bar graph" help="(-w/--bar_width)"/>
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127
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128 <param name="chart_type" type="select" label="Type of chart to plot"
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129 help="(-c/--chart_type)" multiple="True" display="checkboxes">
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130 <option value="area" selected="true">Area</option>
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131 <option value="bar" selected="true">Bar</option>
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132 <option value="pie">Pie</option>
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133 </param>
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134
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135 <param name="include_html_legend" type="boolean" label="Include HTML
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136 legend?" truevalue="--include_html_legend" falsevalue="" checked="False"
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137 help="If checked, the writing of the legend in the html page is
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138 included (-s/--include_html_legend)" />
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139
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140 <param name="label_type" type="select" label="Label type"
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141 help="If the label type is defined as numeric, the x-axis will be
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142 scaled accordingly. Otherwise the x-values will treated categorically
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143 and be evenly spaced(-a/--label_type)">
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144 <option value="categorical" selected="true">Categorical</option>
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145 <option value="numeric">Numeric</option>
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146 </param>
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147 </inputs>
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148
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149 <outputs>
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150 <data name="bar_charts_html_report" format="html"
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151 label="${tool.name} on ${on_string}: Bar charts">
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152 <filter>'bar' in chart_type</filter>
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153 </data>
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154 <data name="pie_charts_html_report" format="html"
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155 label="${tool.name} on ${on_string}: Pie charts">
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156 <filter>'pie' in chart_type</filter>
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157 </data>
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158 <data name="area_charts_html_report" format="html"
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159 label="${tool.name} on ${on_string}: Area charts">
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160 <filter>'area' in chart_type</filter>
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161 </data>
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162 </outputs>
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163
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164 <tests>
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165 <test>
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166 <param name="counts_fname"
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167 value="summarize_taxa_L2.tab"/>
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168 <param name="num_categories" value="20"/>
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169 <param name="background_color" value="white"/>
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170 <param name="dpi" value="80" />
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171 <param name="x_width" value="12" />
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172 <param name="y_height" value="12" />
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173 <param name="bar_width" value="0.75" />
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174 <param name="chart_type" value="area,bar"/>
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175 <param name="include_html_legend" value="" />
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176 <param name="label_type" value="categorical"/>
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177 </test>
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178 </tests>
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179
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180 <help><![CDATA[
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181
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182 **What it does**
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183
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184 This script automates the construction of pie, bar and area charts showing the breakdown of taxonomy by given levels.
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185
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186 More information about this tool is available on
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187 `QIIME documentation <http://qiime.org/scripts/plot_taxa_summary.html>`_.
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188 ]]>
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189 </help>
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190
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191 <citations>
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192 <expand macro="citations" />
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193 </citations>
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194 </tool>