annotate phyloseq_plot_bar.xml @ 3:d0fa6a43c838 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
author iuc
date Fri, 10 Jan 2025 14:58:52 +0000
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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 ]]></command>
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23 <inputs>
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24 <expand macro="phyloseq_input"/>
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25 <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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26 <param name="fill" type="text" label="Fill variable" help="Variable to color the bars (e.g., Genus, Order)." />
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27 <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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28 <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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29 <param name="keepOthers" type="boolean" label="Keep 'Others'" help="Keep OTUs which are not in top X as 'Others'." />
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30 <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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31 <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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32 <param name="width" type="float" value="10" optional="true" label="Plot Width" help="Width of the output plot in inches." />
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33 <param name="height" type="float" value="8" optional="true" label="Plot Height" help="Height of the output plot in inches." />
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34 <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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35 <option value="pdf">PDF</option>
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36 <option value="png">PNG</option>
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37 <option value="jpeg">JPEG</option>
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38 <option value="tiff">TIFF</option>
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39 </param>
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40 </inputs>
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41 <outputs>
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42 <data name="output" format="pdf" label="Bar Chart (PDF)" />
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43 </outputs>
3
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44 <tests>
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45 <!-- Test 1: Basic functionality with x and fill variables -->
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46 <test>
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47 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
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48 <param name="x" value="Property"/>
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49 <param name="fill" value="Phylum"/>
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50 <param name="device" value="pdf"/>
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51 <output name="output" ftype="pdf">
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52 <assert_contents>
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53 <has_text text="%PDF"/>
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54 <has_text text="%%EOF"/>
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55 </assert_contents>
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56 </output>
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57 </test>
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58
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59 <!-- Test 2: TopX filtering and normalization -->
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60 <test>
3
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61 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
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62 <param name="x" value="Property"/>
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63 <param name="fill" value="Genus"/>
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64 <param name="facet" value="SampleType"/>
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65 <param name="topX" value="10"/>
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66 <param name="normalize" value="true"/>
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67 <output name="output" ftype="pdf">
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68 <assert_contents>
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69 <has_text text="%PDF"/>
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70 <has_text text="%%EOF"/>
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71 </assert_contents>
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72 </output>
0
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73 </test>
3
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74 </tests>
0
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75
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76 <help>
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77 **Description**
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78
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79 This tool generates bar charts from a phyloseq object using the `plot_bar` function.
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80
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81 **Inputs**
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82
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83 - **Input**: A phyloseq object in RDS format.
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84 - **X-axis variable**: The variable to use for the x-axis (e.g., Sample, Phylum).
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85 - **Fill variable**: (Optional) The variable to use for the bar fill colors (e.g., Genus, Order).
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86 - **Facet by variable**: (Optional) A variable to facet the bar chart (e.g., SampleType).
3
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87 - **Width and Height**: Dimensions of the plot in inches (default: 10x8).
d0fa6a43c838 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
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88 - **Device**: Output format (e.g., pdf, png, jpeg, tiff).
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ad81e112f4d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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89
ad81e112f4d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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90 **Outputs**
ad81e112f4d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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91
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d0fa6a43c838 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
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92 - A file containing the bar chart in the specified format.
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ad81e112f4d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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93
ad81e112f4d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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94 **Usage Notes**
ad81e112f4d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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95
ad81e112f4d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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96 Ensure that the input file is a valid phyloseq object in RDS format.
ad81e112f4d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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97 </help>
ad81e112f4d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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98 <expand macro="citations"/>
ad81e112f4d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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99 </tool>