Mercurial > repos > iuc > phyloseq_plot_bar

comparison phyloseq_plot_bar.xml @ 3:7b9b6147156b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
author iuc
date Fri, 10 Jan 2025 14:57:59 +0000
parents 7300d19148d7
children 4b5439de35c8
comparison
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2:ae367e1b542a 3:7b9b6147156b
10 --input '$input' 10 --input '$input'
11 --x '$x' 11 --x '$x'
12 --fill '$fill' 12 --fill '$fill'
13 --facet '${facet}' 13 --facet '${facet}'
14 --output '$output' 14 --output '$output'
15 --topX '${topX}'
16 --keepOthers '${keepOthers}'
17 --keepNonAssigned '${keepNonAssigned}'
18 --normalize '${normalize}'
19 --width '${width}'
20 --height '${height}'
21 --device '${device}'
15 ]]></command> 22 ]]></command>
16 <inputs> 23 <inputs>
17 <expand macro="phyloseq_input"/> 24 <expand macro="phyloseq_input"/>
18 <param name="x" type="text" label="X-axis variable" help="Variable for the x-axis (e.g., Sample, Phylum)" /> 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." />
19 <param name="fill" type="text" label="Fill variable" help="Variable to color the bars (e.g., Genus, Order)" /> 26 <param name="fill" type="text" label="Fill variable" help="Variable to color the bars (e.g., Genus, Order)." />
20 <param name="facet" type="text" optional="true" label="Facet by variable" help="Optional: Variable to facet the chart by (e.g., SampleType)" /> 27 <param name="facet" type="text" optional="true" label="Facet by variable" help="Variable to facet the chart by (e.g., SampleType)." />
28 <param name="topX" value="10" type="integer" optional="true" label="Top X" help="Only show the ranks with the top X abundance." />
29 <param name="keepOthers" type="boolean" label="Keep 'Others'" help="Keep OTUs which are not in top X as 'Others'." />
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'." />
31 <param name="normalize" type="boolean" label="Normalize" help="Normalize abundances to sum to 100%. Normalization is performed before Top X selection." />
32 <param name="width" type="float" value="10" optional="true" label="Plot Width" help="Width of the output plot in inches." />
33 <param name="height" type="float" value="8" optional="true" label="Plot Height" help="Height of the output plot in inches." />
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.">
35 <option value="pdf">PDF</option>
36 <option value="png">PNG</option>
37 <option value="jpeg">JPEG</option>
38 <option value="tiff">TIFF</option>
39 </param>
21 </inputs> 40 </inputs>
22 <outputs> 41 <outputs>
23 <data name="output" format="pdf" label="Bar Chart (PDF)" /> 42 <data name="output" format="pdf" label="Bar Chart (PDF)" />
24 </outputs> 43 </outputs>
25 <tests> 44 <tests>
26 <!-- Test 1: Default parameters --> 45 <!-- Test 1: Basic functionality with x and fill variables -->
27 <test> 46 <test>
28 <param name="input" value="output.phyloseq" ftype="phyloseq"/> 47 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
29 <param name="x" value="Property"/> 48 <param name="x" value="Property"/>
30 <param name="fill" value="Number"/> 49 <param name="fill" value="Phylum"/>
31 <param name="facet" value="Property"/> 50 <param name="device" value="pdf"/>
32 <output name="output" ftype="pdf"> 51 <output name="output" ftype="pdf">
33 <assert_contents> 52 <assert_contents>
34 <has_text text="%PDF"/> 53 <has_text text="%PDF"/>
35 <has_text text="%%EOF"/> 54 <has_text text="%%EOF"/>
36 </assert_contents> 55 </assert_contents>
37 </output> 56 </output>
38 </test> 57 </test>
39 <!-- Test 2: Valid parameters without facet --> 58
59 <!-- Test 2: TopX filtering and normalization -->
40 <test> 60 <test>
41 <param name="input" value="output.phyloseq" ftype="phyloseq"/> 61 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
42 <param name="x" value="Property"/> 62 <param name="x" value="Property"/>
43 <param name="fill" value="Number"/> 63 <param name="fill" value="Genus"/>
44 <param name="facet" value=""/> 64 <param name="facet" value="SampleType"/>
45 <output name="output" ftype="pdf"> 65 <param name="topX" value="10"/>
46 <assert_contents> 66 <param name="normalize" value="true"/>
47 <has_text text="%PDF"/> 67 <output name="output" ftype="pdf">
48 <has_text text="%%EOF"/> 68 <assert_contents>
49 </assert_contents> 69 <has_text text="%PDF"/>
50 </output> 70 <has_text text="%%EOF"/>
71 </assert_contents>
72 </output>
51 </test> 73 </test>
52 </tests> 74 </tests>
53 75
54 <help> 76 <help>
55 **Description** 77 **Description**
56 78
57 This tool generates bar charts from a phyloseq object using the `plot_bar` function. 79 This tool generates bar charts from a phyloseq object using the `plot_bar` function.
60 82
61 - **Input**: A phyloseq object in RDS format. 83 - **Input**: A phyloseq object in RDS format.
62 - **X-axis variable**: The variable to use for the x-axis (e.g., Sample, Phylum). 84 - **X-axis variable**: The variable to use for the x-axis (e.g., Sample, Phylum).
63 - **Fill variable**: (Optional) The variable to use for the bar fill colors (e.g., Genus, Order). 85 - **Fill variable**: (Optional) The variable to use for the bar fill colors (e.g., Genus, Order).
64 - **Facet by variable**: (Optional) A variable to facet the bar chart (e.g., SampleType). 86 - **Facet by variable**: (Optional) A variable to facet the bar chart (e.g., SampleType).
87 - **Width and Height**: Dimensions of the plot in inches (default: 10x8).
88 - **Device**: Output format (e.g., pdf, png, jpeg, tiff).
65 89
66 **Outputs** 90 **Outputs**
67 91
68 - A PDF file containing the bar chart. 92 - A file containing the bar chart in the specified format.
69 93
70 **Usage Notes** 94 **Usage Notes**
71 95
72 Ensure that the input file is a valid phyloseq object in RDS format. 96 Ensure that the input file is a valid phyloseq object in RDS format.
73 </help> 97 </help>
74 <expand macro="citations"/> 98 <expand macro="citations"/>
75 </tool> 99 </tool>
76