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comparison phyloseq_plot_bar.xml @ 0:7300d19148d7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
author iuc
date Tue, 03 Dec 2024 17:44:59 +0000
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1 <tool id="phyloseq_plot_bar" name="Phyloseq: Bar Chart" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Generate bar charts from a phyloseq object</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 Rscript '${__tool_directory__}/phyloseq_plot_bar.R'
10 --input '$input'
11 --x '$x'
12 --fill '$fill'
13 --facet '${facet}'
14 --output '$output'
15 ]]></command>
16 <inputs>
17 <expand macro="phyloseq_input"/>
18 <param name="x" type="text" label="X-axis variable" help="Variable for the x-axis (e.g., Sample, Phylum)" />
19 <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)" />
21 </inputs>
22 <outputs>
23 <data name="output" format="pdf" label="Bar Chart (PDF)" />
24 </outputs>
25 <tests>
26 <!-- Test 1: Default parameters -->
27 <test>
28 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
29 <param name="x" value="Property"/>
30 <param name="fill" value="Number"/>
31 <param name="facet" value="Property"/>
32 <output name="output" ftype="pdf">
33 <assert_contents>
34 <has_text text="%PDF"/>
35 <has_text text="%%EOF"/>
36 </assert_contents>
37 </output>
38 </test>
39 <!-- Test 2: Valid parameters without facet -->
40 <test>
41 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
42 <param name="x" value="Property"/>
43 <param name="fill" value="Number"/>
44 <param name="facet" value=""/>
45 <output name="output" ftype="pdf">
46 <assert_contents>
47 <has_text text="%PDF"/>
48 <has_text text="%%EOF"/>
49 </assert_contents>
50 </output>
51 </test>
52 </tests>
53
54 <help>
55 **Description**
56
57 This tool generates bar charts from a phyloseq object using the `plot_bar` function.
58
59 **Inputs**
60
61 - **Input**: A phyloseq object in RDS format.
62 - **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).
64 - **Facet by variable**: (Optional) A variable to facet the bar chart (e.g., SampleType).
65
66 **Outputs**
67
68 - A PDF file containing the bar chart.
69
70 **Usage Notes**
71
72 Ensure that the input file is a valid phyloseq object in RDS format.
73 </help>
74 <expand macro="citations"/>
75 </tool>
76