Mercurial > repos > iuc > phyloseq_plot_bar

annotate phyloseq_plot_bar.xml @ 6:0150f6dcd750 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit a5ae2f86b2955290a4c81ab234f02cc51020f970
author iuc
date Thu, 13 Mar 2025 09:47:28 +0000
parents 4b5439de35c8
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1 <tool id="phyloseq_plot_bar" name="Phyloseq: Bar Chart" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Generate bar charts from a phyloseq object</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 Rscript '${__tool_directory__}/phyloseq_plot_bar.R'
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10 --input '$input'
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11 --x '$x'
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12 --fill '$fill'
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13 --facet '$facet'
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14 --topX '$topX'
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15 '$keepOthers'
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16 '$keepNonAssigned'
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17 '$normalize'
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18 '$normalize_x'
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19 '$nolines'
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20 --width '$width'
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21 --height '$height'
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22 --device '$device'
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23 --output '$output'
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24 ]]></command>
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25 <inputs>
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26 <expand macro="phyloseq_input"/>
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27 <param name="x" type="text" optional="true" label="X-axis variable" help="Variable for the x-axis (Metadata columns). If not specified, the Samples are taken." />
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28 <param name="fill" type="text" label="Fill variable" help="Variable to color the bars (e.g., Genus, Species). Use 'ASV' as argument to show each OTU/ASV." />
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29 <param name="facet" type="text" optional="true" label="Facet by variable" help="Variable to facet the chart by (e.g., SampleType)." />
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30 <param name="topX" value="10" type="integer" optional="true" label="Top X" help="Only show the ranks with the top X abundance." />
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31 <param name="keepOthers" type="boolean" truevalue="--keepOthers" falsevalue="" label="Keep 'Others'" help="Keep OTUs which are not in top X as 'Others'." />
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32 <param name="keepNonAssigned" type="boolean" truevalue="--keepNonAssigned" falsevalue="" label="Keep 'Not Assigned'" help="Keep OTUs that are not assigned at this rank and label as 'Not Assigned'." />
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33 <param name="normalize" type="boolean" truevalue="--normalize" falsevalue="" label="Normalize" help="Normalize abundances to sum to 100%. Normalization is performed before Top X selection." />
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34 <param name="normalize_x" type="boolean" truevalue="--normalize_x" falsevalue="" label="Normalize x" help="Normalize abundances of the x group to sum to 100%. Normalization is performed before Top X selection. Ignores facetting!" />
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35 <param name="nolines" type="boolean" truevalue="--nolines" falsevalue="" label="Remove Separation Lines" help="Do not add OTU separation lines in the bars." />
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36 <param name="width" type="float" value="10" optional="true" label="Plot Width" help="Width of the output plot in inches." />
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37 <param name="height" type="float" value="8" optional="true" label="Plot Height" help="Height of the output plot in inches." />
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38 <param name="device" type="select" value="pdf" label="Output Device" help="File format to use for the output file. ">
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39 <option value="pdf">PDF</option>
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40 <option value="png">PNG</option>
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41 <option value="jpg">JEG</option>
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42 <option value="tiff">TIFF</option>
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43 </param>
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44 </inputs>
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45 <outputs>
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46 <data name="output" format="pdf" label="Bar Chart (${device})">
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47 <change_format>
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48 <when input="device" format="pdf" value="pdf"/>
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49 <when input="device" format="png" value="png"/>
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50 <when input="device" format="jpg" value="jpg"/>
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51 <when input="device" format="tiff" value="tiff"/>
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52 </change_format>
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53 </data>
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54 </outputs>
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55
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56 <tests>
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57 <!-- Test 1: Basic functionality with x and fill variables -->
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58 <test>
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59 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
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60 <param name="x" value="Property"/>
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61 <param name="fill" value="Phylum"/>
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62 <param name="device" value="png"/>
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63 <output name="output" file="expected_output_01.png" ftype="png" compare="image_diff"/>
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64 </test>
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66 <!-- Test 2: TopX filtering and normalization -->
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67 <test>
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68 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
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69 <param name="x" value="Property"/>
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70 <param name="fill" value="Genus"/>
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71 <param name="facet" value="Number"/>
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72 <param name="topX" value="10"/>
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73 <param name="normalize" value="true"/>
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74 <param name="device" value="png"/>
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75 <output name="output" file="expected_output_02.png" ftype="png" compare="image_diff"/>
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76 </test>
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77
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79 <!-- Test 3: without OTU lines, Others and non assigned -->
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80 <test>
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81 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
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82 <param name="x" value="Sample"/>
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83 <param name="fill" value="Genus"/>
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84 <param name="facet" value=""/>
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85 <param name="topX" value="10"/>
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86 <param name="normalize" value="false"/>
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87 <param name="keepOthers" value="true"/>
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88 <param name="keepNonAssigned" value="false"/>
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89 <param name="nolines" value="true"/>
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90 <param name="device" value="png"/>
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91 <output name="output" file="expected_output_03.png" ftype="png" compare="image_diff"/>
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92 </test>
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93
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94 <!-- Test 4: with normalization, Others and non assigned -->
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95 <test>
5
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96 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
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97 <param name="x" value="Sample"/>
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98 <param name="fill" value="Genus"/>
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99 <param name="facet" value=""/>
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100 <param name="topX" value="10"/>
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101 <param name="normalize" value="true"/>
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102 <param name="keepOthers" value="true"/>
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103 <param name="keepNonAssigned" value="true"/>
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104 <param name="nolines" value="false"/>
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105 <param name="device" value="png"/>
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106 <output name="output" file="expected_output_04.png" ftype="png" compare="image_diff"/>
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107 </test>
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108
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109 <!-- Test 5: with normalization, Others and non assigned, normalization x -->
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110 <test>
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111 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
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112 <param name="x" value="Property"/>
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113 <param name="fill" value="Genus"/>
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114 <param name="facet" value=""/>
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115 <param name="topX" value="10"/>
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116 <param name="normalize" value="true"/>
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117 <param name="keepOthers" value="true"/>
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118 <param name="keepNonAssigned" value="true"/>
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119 <param name="normalize_x" value="true"/>
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120 <param name="nolines" value="false"/>
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121 <param name="device" value="png"/>
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122 <output name="output" file="expected_output_05.png" ftype="png" compare="image_diff"/>
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123 </test>
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124
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125 <!-- Test 6: Minimal -->
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126 <test>
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127 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
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128 <param name="device" value="png"/>
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129 <output name="output" file="expected_output_06.png" ftype="png" compare="image_diff"/>
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130 </test>
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131
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132 </tests>
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133
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134 <help>
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135 <![CDATA[
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136 **Description**
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137
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138 This tool generates bar charts from a phyloseq object using the 'plot_bar' function in R.
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139 It allows filtering, normalization, and customization of plots for visualizing microbial community composition.
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140
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141 **Inputs**
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142
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143 - **Input**: A phyloseq object in RDS format.
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144
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145 - **X-axis variable**: The variable to use for the x-axis (Metadata columns).
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146
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147 - **Fill variable**: (Optional) The variable to use for the bar fill colors (e.g., Genus, Species).
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148
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149 - **Facet by variable**: (Optional) A variable to facet the bar chart (e.g., SampleType).
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150
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151 - **Top X**: Display only the top X most abundant taxa.
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152
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153 - **Keep 'Others'**: Group non-top taxa as 'Others'.
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154
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155 - **Keep 'Not Assigned'**: Retain unassigned taxa labeled as 'Not Assigned'.
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156
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157 - **Normalize**: Normalize abundances to sum to 100%.
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158
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159 - **Remove Separation Lines**: Do not add OTU separation lines in the bars.
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160
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161 - **Width and Height**: Dimensions of the plot in inches (default: 10x8).
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162
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163 - **Device**: Output format (e.g., pdf, png, jpg, tiff).
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164
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165 **Outputs**
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166
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167 - A file containing the bar chart in the specified format.
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168
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169 **Usage Notes**
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170
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171 Ensure that the input file is a valid phyloseq object in RDS format.
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172
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173 **Examples**
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174
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175 - *Basic Bar Plot with Others and Not Assigned and with separation lines*
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176
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177 .. image:: $PATH_TO_IMAGES/standard_plot.png
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178 :width: 515
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179 :height: 395
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180
6
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181 - *Faceted Plot*
0
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182
6
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183 .. image:: $PATH_TO_IMAGES/facet_plot.png
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184 :width: 515
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185 :height: 395
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186
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187 - *ASV as fill input and removed separation lines*
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188
6
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189 .. image:: $PATH_TO_IMAGES/asv_fill_plot.png
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190 :width: 515
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191 :height: 395
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192 ]]>
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193 </help>
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194
0
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195 <expand macro="citations"/>
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196 </tool>