Mercurial > repos > iuc > phyloseq_plot_bar

annotate phyloseq_plot_bar.xml @ 5:4b5439de35c8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d6888da7aba38b97f6cb827355f2de436565684a
author iuc
date Tue, 04 Feb 2025 14:38:03 +0000
parents 7b9b6147156b
children 0150f6dcd750
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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 '${facet}'
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14 --output '$output'
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15 --topX '${topX}'
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16 --keepOthers '${keepOthers}'
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17 --keepNonAssigned '${keepNonAssigned}'
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18 --normalize '${normalize}'
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19 --width '${width}'
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20 --height '${height}'
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21 --device '${device}'
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22 --nolines '${nolines}'
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23 ]]></command>
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24 <inputs>
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25 <expand macro="phyloseq_input"/>
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26 <param name="x" type="text" optional="true" label="X-axis variable" help="Variable for the x-axis (e.g., Sample, Phylum). If not specified, the Samples are taken." />
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27 <param name="fill" type="text" label="Fill variable" help="Variable to color the bars (e.g., Genus, Order)." />
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28 <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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29 <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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30 <param name="keepOthers" type="boolean" label="Keep 'Others'" help="Keep OTUs which are not in top X as 'Others'." />
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31 <param name="keepNonAssigned" type="boolean" label="Keep Non Assigned" help="Keep OTUs that are not assigned at this rank and label as 'Not Assigned'." />
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32 <param name="normalize" type="boolean" label="Normalize" help="Normalize abundances to sum to 100%. Normalization is performed before Top X selection." />
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33 <param name="width" type="float" value="10" optional="true" label="Plot Width" help="Width of the output plot in inches." />
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34 <param name="height" type="float" value="8" optional="true" label="Plot Height" help="Height of the output plot in inches." />
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35 <param name="device" type="select" value="pdf" label="Output Device" help="Device to use for the output file. Options include pdf, png, and others.">
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36 <option value="pdf">PDF</option>
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37 <option value="png">PNG</option>
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38 <option value="jpeg">JPEG</option>
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39 <option value="tiff">TIFF</option>
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40 </param>
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41 <param name="nolines" type="boolean" label="Remove Separation Lines" help="Do not add separation lines between bars in the chart." />
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42 </inputs>
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43 <outputs>
5
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44 <data name="output" format="pdf" label="Bar Chart (${device})">
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45 <change_format>
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46 <when format="pdf" value="pdf"/>
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47 <when format="png" value="png"/>
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48 <when format="jpeg" value="jpeg"/>
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49 <when format="tiff" value="tiff"/>
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50 </change_format>
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51
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52 </data>
0
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53 </outputs>
5
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54
3
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55 <tests>
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56 <!-- Test 1: Basic functionality with x and fill variables -->
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57 <test>
3
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58 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
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59 <param name="x" value="Property"/>
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60 <param name="fill" value="Phylum"/>
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61 <param name="device" value="pdf"/>
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62 <output name="output" ftype="pdf">
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63 <assert_contents>
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64 <has_text text="%PDF"/>
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65 <has_text text="%%EOF"/>
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66 </assert_contents>
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67 </output>
0
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68 </test>
3
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69
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70 <!-- Test 2: TopX filtering and normalization -->
0
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71 <test>
3
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72 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
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73 <param name="x" value="Property"/>
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74 <param name="fill" value="Genus"/>
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75 <param name="facet" value="SampleType"/>
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76 <param name="topX" value="10"/>
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77 <param name="normalize" value="true"/>
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78 <output name="output" ftype="pdf">
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79 <assert_contents>
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80 <has_text text="%PDF"/>
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81 <has_text text="%%EOF"/>
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82 </assert_contents>
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83 </output>
0
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84 </test>
5
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85
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86 <!-- Test 3: without OTU lines, Others and non assigned -->
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87 <test>
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88 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
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89 <param name="x" value="Sample"/>
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90 <param name="fill" value="Genus"/>
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91 <param name="facet" value=""/>
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92 <param name="topX" value="10"/>
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93 <param name="normalize" value="false"/>
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94 <param name="keepOthers" value="false"/>
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95 <param name="keepNonAssigned" value="false"/>
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96 <param name="nolines" value="true"/>
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97 <param name="device" value="pdf"/>
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98 <output name="output" file="expected_output.pdf" ftype="pdf" compare="sim_size"/>
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99 </test>
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100
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101 <!-- Test 4: with normalization, Others and non assigned -->
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102 <test>
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103 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
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104 <param name="x" value="Sample"/>
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105 <param name="fill" value="Genus"/>
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106 <param name="facet" value=""/>
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107 <param name="topX" value="10"/>
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108 <param name="normalize" value="true"/>
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109 <param name="keepOthers" value="true"/>
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110 <param name="keepNonAssigned" value="true"/>
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111 <param name="nolines" value="false"/>
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112 <param name="device" value="pdf"/>
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113 <output name="output" file="expected_output_normalize.pdf" ftype="pdf" compare="sim_size"/>
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114 </test>
3
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115 </tests>
0
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116
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117 <help>
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118 **Description**
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119
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120 This tool generates bar charts from a phyloseq object using the `plot_bar` function.
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121
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122 **Inputs**
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123
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124 - **Input**: A phyloseq object in RDS format.
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125 - **X-axis variable**: The variable to use for the x-axis (e.g., Sample, Phylum).
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126 - **Fill variable**: (Optional) The variable to use for the bar fill colors (e.g., Genus, Order).
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127 - **Facet by variable**: (Optional) A variable to facet the bar chart (e.g., SampleType).
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128 - **Width and Height**: Dimensions of the plot in inches (default: 10x8).
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129 - **Device**: Output format (e.g., pdf, png, jpeg, tiff).
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130
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131 **Outputs**
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132
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133 - A file containing the bar chart in the specified format.
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134
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135 **Usage Notes**
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136
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137 Ensure that the input file is a valid phyloseq object in RDS format.
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138 </help>
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139 <expand macro="citations"/>
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140 </tool>