Mercurial > repos > iuc > phyloseq_plot_bar

comparison 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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4:da638ad23cd4 5:4b5439de35c8
17 --keepNonAssigned '${keepNonAssigned}' 17 --keepNonAssigned '${keepNonAssigned}'
18 --normalize '${normalize}' 18 --normalize '${normalize}'
19 --width '${width}' 19 --width '${width}'
20 --height '${height}' 20 --height '${height}'
21 --device '${device}' 21 --device '${device}'
22 --nolines '${nolines}'
22 ]]></command> 23 ]]></command>
23 <inputs> 24 <inputs>
24 <expand macro="phyloseq_input"/> 25 <expand macro="phyloseq_input"/>
25 <param name="x" type="text" optional="true" label="X-axis variable" help="Variable for the x-axis (e.g., Sample, Phylum). If not specified, the Samples are taken." /> 26 <param name="x" type="text" optional="true" label="X-axis variable" help="Variable for the x-axis (e.g., Sample, Phylum). If not specified, the Samples are taken." />
26 <param name="fill" type="text" label="Fill variable" help="Variable to color the bars (e.g., Genus, Order)." /> 27 <param name="fill" type="text" label="Fill variable" help="Variable to color the bars (e.g., Genus, Order)." />
35 <option value="pdf">PDF</option> 36 <option value="pdf">PDF</option>
36 <option value="png">PNG</option> 37 <option value="png">PNG</option>
37 <option value="jpeg">JPEG</option> 38 <option value="jpeg">JPEG</option>
38 <option value="tiff">TIFF</option> 39 <option value="tiff">TIFF</option>
39 </param> 40 </param>
41 <param name="nolines" type="boolean" label="Remove Separation Lines" help="Do not add separation lines between bars in the chart." />
40 </inputs> 42 </inputs>
41 <outputs> 43 <outputs>
42 <data name="output" format="pdf" label="Bar Chart (PDF)" /> 44 <data name="output" format="pdf" label="Bar Chart (${device})">
45 <change_format>
46 <when format="pdf" value="pdf"/>
47 <when format="png" value="png"/>
48 <when format="jpeg" value="jpeg"/>
49 <when format="tiff" value="tiff"/>
50 </change_format>
51
52 </data>
43 </outputs> 53 </outputs>
54
44 <tests> 55 <tests>
45 <!-- Test 1: Basic functionality with x and fill variables --> 56 <!-- Test 1: Basic functionality with x and fill variables -->
46 <test> 57 <test>
47 <param name="input" value="output.phyloseq" ftype="phyloseq"/> 58 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
48 <param name="x" value="Property"/> 59 <param name="x" value="Property"/>
69 <has_text text="%PDF"/> 80 <has_text text="%PDF"/>
70 <has_text text="%%EOF"/> 81 <has_text text="%%EOF"/>
71 </assert_contents> 82 </assert_contents>
72 </output> 83 </output>
73 </test> 84 </test>
85
86 <!-- Test 3: without OTU lines, Others and non assigned -->
87 <test>
88 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
89 <param name="x" value="Sample"/>
90 <param name="fill" value="Genus"/>
91 <param name="facet" value=""/>
92 <param name="topX" value="10"/>
93 <param name="normalize" value="false"/>
94 <param name="keepOthers" value="false"/>
95 <param name="keepNonAssigned" value="false"/>
96 <param name="nolines" value="true"/>
97 <param name="device" value="pdf"/>
98 <output name="output" file="expected_output.pdf" ftype="pdf" compare="sim_size"/>
99 </test>
100
101 <!-- Test 4: with normalization, Others and non assigned -->
102 <test>
103 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
104 <param name="x" value="Sample"/>
105 <param name="fill" value="Genus"/>
106 <param name="facet" value=""/>
107 <param name="topX" value="10"/>
108 <param name="normalize" value="true"/>
109 <param name="keepOthers" value="true"/>
110 <param name="keepNonAssigned" value="true"/>
111 <param name="nolines" value="false"/>
112 <param name="device" value="pdf"/>
113 <output name="output" file="expected_output_normalize.pdf" ftype="pdf" compare="sim_size"/>
114 </test>
74 </tests> 115 </tests>
75 116
76 <help> 117 <help>
77 **Description** 118 **Description**
78 119