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comparison phyloseq_plot_bar.xml @ 6:0150f6dcd750 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit a5ae2f86b2955290a4c81ab234f02cc51020f970
author iuc
date Thu, 13 Mar 2025 09:47:28 +0000
parents 4b5439de35c8
children
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5:4b5439de35c8 6:0150f6dcd750
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 Rscript '${__tool_directory__}/phyloseq_plot_bar.R' 9 Rscript '${__tool_directory__}/phyloseq_plot_bar.R'
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 --topX '$topX'
15 '$keepOthers'
16 '$keepNonAssigned'
17 '$normalize'
18 '$normalize_x'
19 '$nolines'
20 --width '$width'
21 --height '$height'
22 --device '$device'
14 --output '$output' 23 --output '$output'
15 --topX '${topX}'
16 --keepOthers '${keepOthers}'
17 --keepNonAssigned '${keepNonAssigned}'
18 --normalize '${normalize}'
19 --width '${width}'
20 --height '${height}'
21 --device '${device}'
22 --nolines '${nolines}'
23 ]]></command> 24 ]]></command>
24 <inputs> 25 <inputs>
25 <expand macro="phyloseq_input"/> 26 <expand macro="phyloseq_input"/>
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." /> 27 <param name="x" type="text" optional="true" label="X-axis variable" help="Variable for the x-axis (Metadata columns). If not specified, the Samples are taken." />
27 <param name="fill" type="text" label="Fill variable" help="Variable to color the bars (e.g., Genus, Order)." /> 28 <param name="fill" type="text" label="Fill variable" help="Variable to color the bars (e.g., Genus, Species). Use 'ASV' as argument to show each OTU/ASV." />
28 <param name="facet" type="text" optional="true" label="Facet by variable" help="Variable to facet the chart by (e.g., SampleType)." /> 29 <param name="facet" type="text" optional="true" label="Facet by variable" help="Variable to facet the chart by (e.g., SampleType)." />
29 <param name="topX" value="10" type="integer" optional="true" label="Top X" help="Only show the ranks with the top X abundance." /> 30 <param name="topX" value="10" type="integer" optional="true" label="Top X" help="Only show the ranks with the top X abundance." />
30 <param name="keepOthers" type="boolean" label="Keep 'Others'" help="Keep OTUs which are not in top X as 'Others'." /> 31 <param name="keepOthers" type="boolean" truevalue="--keepOthers" falsevalue="" label="Keep 'Others'" help="Keep OTUs which are not in top X as 'Others'." />
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'." /> 32 <param name="keepNonAssigned" type="boolean" truevalue="--keepNonAssigned" falsevalue="" label="Keep 'Not Assigned'" help="Keep OTUs that are not assigned at this rank and label as 'Not Assigned'." />
32 <param name="normalize" type="boolean" label="Normalize" help="Normalize abundances to sum to 100%. Normalization is performed before Top X selection." /> 33 <param name="normalize" type="boolean" truevalue="--normalize" falsevalue="" label="Normalize" help="Normalize abundances to sum to 100%. Normalization is performed before Top X selection." />
34 <param name="normalize_x" type="boolean" truevalue="--normalize_x" falsevalue="" label="Normalize x" help="Normalize abundances of the x group to sum to 100%. Normalization is performed before Top X selection. Ignores facetting!" />
35 <param name="nolines" type="boolean" truevalue="--nolines" falsevalue="" label="Remove Separation Lines" help="Do not add OTU separation lines in the bars." />
33 <param name="width" type="float" value="10" optional="true" label="Plot Width" help="Width of the output plot in inches." /> 36 <param name="width" type="float" value="10" optional="true" label="Plot Width" help="Width of the output plot in inches." />
34 <param name="height" type="float" value="8" optional="true" label="Plot Height" help="Height of the output plot in inches." /> 37 <param name="height" type="float" value="8" optional="true" label="Plot Height" help="Height of the output plot in inches." />
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."> 38 <param name="device" type="select" value="pdf" label="Output Device" help="File format to use for the output file. ">
36 <option value="pdf">PDF</option> 39 <option value="pdf">PDF</option>
37 <option value="png">PNG</option> 40 <option value="png">PNG</option>
38 <option value="jpeg">JPEG</option> 41 <option value="jpg">JEG</option>
39 <option value="tiff">TIFF</option> 42 <option value="tiff">TIFF</option>
40 </param> 43 </param>
41 <param name="nolines" type="boolean" label="Remove Separation Lines" help="Do not add separation lines between bars in the chart." />
42 </inputs> 44 </inputs>
43 <outputs> 45 <outputs>
44 <data name="output" format="pdf" label="Bar Chart (${device})"> 46 <data name="output" format="pdf" label="Bar Chart (${device})">
45 <change_format> 47 <change_format>
46 <when format="pdf" value="pdf"/> 48 <when input="device" format="pdf" value="pdf"/>
47 <when format="png" value="png"/> 49 <when input="device" format="png" value="png"/>
48 <when format="jpeg" value="jpeg"/> 50 <when input="device" format="jpg" value="jpg"/>
49 <when format="tiff" value="tiff"/> 51 <when input="device" format="tiff" value="tiff"/>
50 </change_format> 52 </change_format>
51
52 </data> 53 </data>
53 </outputs> 54 </outputs>
54 55
55 <tests> 56 <tests>
56 <!-- Test 1: Basic functionality with x and fill variables --> 57 <!-- Test 1: Basic functionality with x and fill variables -->
57 <test> 58 <test>
58 <param name="input" value="output.phyloseq" ftype="phyloseq"/> 59 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
59 <param name="x" value="Property"/> 60 <param name="x" value="Property"/>
60 <param name="fill" value="Phylum"/> 61 <param name="fill" value="Phylum"/>
61 <param name="device" value="pdf"/> 62 <param name="device" value="png"/>
62 <output name="output" ftype="pdf"> 63 <output name="output" file="expected_output_01.png" ftype="png" compare="image_diff"/>
63 <assert_contents>
64 <has_text text="%PDF"/>
65 <has_text text="%%EOF"/>
66 </assert_contents>
67 </output>
68 </test> 64 </test>
69 65
70 <!-- Test 2: TopX filtering and normalization --> 66 <!-- Test 2: TopX filtering and normalization -->
71 <test> 67 <test>
72 <param name="input" value="output.phyloseq" ftype="phyloseq"/> 68 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
73 <param name="x" value="Property"/> 69 <param name="x" value="Property"/>
74 <param name="fill" value="Genus"/> 70 <param name="fill" value="Genus"/>
75 <param name="facet" value="SampleType"/> 71 <param name="facet" value="Number"/>
76 <param name="topX" value="10"/> 72 <param name="topX" value="10"/>
77 <param name="normalize" value="true"/> 73 <param name="normalize" value="true"/>
78 <output name="output" ftype="pdf"> 74 <param name="device" value="png"/>
79 <assert_contents> 75 <output name="output" file="expected_output_02.png" ftype="png" compare="image_diff"/>
80 <has_text text="%PDF"/>
81 <has_text text="%%EOF"/>
82 </assert_contents>
83 </output>
84 </test> 76 </test>
85 77
86 <!-- Test 3: without OTU lines, Others and non assigned --> 78
87 <test> 79 <!-- Test 3: without OTU lines, Others and non assigned -->
80 <test>
88 <param name="input" value="output.phyloseq" ftype="phyloseq"/> 81 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
89 <param name="x" value="Sample"/> 82 <param name="x" value="Sample"/>
90 <param name="fill" value="Genus"/> 83 <param name="fill" value="Genus"/>
91 <param name="facet" value=""/> 84 <param name="facet" value=""/>
92 <param name="topX" value="10"/> 85 <param name="topX" value="10"/>
93 <param name="normalize" value="false"/> 86 <param name="normalize" value="false"/>
94 <param name="keepOthers" value="false"/> 87 <param name="keepOthers" value="true"/>
95 <param name="keepNonAssigned" value="false"/> 88 <param name="keepNonAssigned" value="false"/>
96 <param name="nolines" value="true"/> 89 <param name="nolines" value="true"/>
97 <param name="device" value="pdf"/> 90 <param name="device" value="png"/>
98 <output name="output" file="expected_output.pdf" ftype="pdf" compare="sim_size"/> 91 <output name="output" file="expected_output_03.png" ftype="png" compare="image_diff"/>
99 </test> 92 </test>
100 93
101 <!-- Test 4: with normalization, Others and non assigned --> 94 <!-- Test 4: with normalization, Others and non assigned -->
102 <test> 95 <test>
103 <param name="input" value="output.phyloseq" ftype="phyloseq"/> 96 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
104 <param name="x" value="Sample"/> 97 <param name="x" value="Sample"/>
105 <param name="fill" value="Genus"/> 98 <param name="fill" value="Genus"/>
106 <param name="facet" value=""/> 99 <param name="facet" value=""/>
107 <param name="topX" value="10"/> 100 <param name="topX" value="10"/>
108 <param name="normalize" value="true"/> 101 <param name="normalize" value="true"/>
109 <param name="keepOthers" value="true"/> 102 <param name="keepOthers" value="true"/>
110 <param name="keepNonAssigned" value="true"/> 103 <param name="keepNonAssigned" value="true"/>
111 <param name="nolines" value="false"/> 104 <param name="nolines" value="false"/>
112 <param name="device" value="pdf"/> 105 <param name="device" value="png"/>
113 <output name="output" file="expected_output_normalize.pdf" ftype="pdf" compare="sim_size"/> 106 <output name="output" file="expected_output_04.png" ftype="png" compare="image_diff"/>
114 </test> 107 </test>
108
109 <!-- Test 5: with normalization, Others and non assigned, normalization x -->
110 <test>
111 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
112 <param name="x" value="Property"/>
113 <param name="fill" value="Genus"/>
114 <param name="facet" value=""/>
115 <param name="topX" value="10"/>
116 <param name="normalize" value="true"/>
117 <param name="keepOthers" value="true"/>
118 <param name="keepNonAssigned" value="true"/>
119 <param name="normalize_x" value="true"/>
120 <param name="nolines" value="false"/>
121 <param name="device" value="png"/>
122 <output name="output" file="expected_output_05.png" ftype="png" compare="image_diff"/>
123 </test>
124
125 <!-- Test 6: Minimal -->
126 <test>
127 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
128 <param name="device" value="png"/>
129 <output name="output" file="expected_output_06.png" ftype="png" compare="image_diff"/>
130 </test>
131
115 </tests> 132 </tests>
116 133
117 <help> 134 <help>
118 **Description** 135 <![CDATA[
136 **Description**
119 137
120 This tool generates bar charts from a phyloseq object using the `plot_bar` function. 138 This tool generates bar charts from a phyloseq object using the 'plot_bar' function in R.
139 It allows filtering, normalization, and customization of plots for visualizing microbial community composition.
121 140
122 **Inputs** 141 **Inputs**
123 142
124 - **Input**: A phyloseq object in RDS format. 143 - **Input**: A phyloseq object in RDS format.
125 - **X-axis variable**: The variable to use for the x-axis (e.g., Sample, Phylum).
126 - **Fill variable**: (Optional) The variable to use for the bar fill colors (e.g., Genus, Order).
127 - **Facet by variable**: (Optional) A variable to facet the bar chart (e.g., SampleType).
128 - **Width and Height**: Dimensions of the plot in inches (default: 10x8).
129 - **Device**: Output format (e.g., pdf, png, jpeg, tiff).
130 144
131 **Outputs** 145 - **X-axis variable**: The variable to use for the x-axis (Metadata columns).
132 146
133 - A file containing the bar chart in the specified format. 147 - **Fill variable**: (Optional) The variable to use for the bar fill colors (e.g., Genus, Species).
134 148
135 **Usage Notes** 149 - **Facet by variable**: (Optional) A variable to facet the bar chart (e.g., SampleType).
136 150
137 Ensure that the input file is a valid phyloseq object in RDS format. 151 - **Top X**: Display only the top X most abundant taxa.
138 </help> 152
153 - **Keep 'Others'**: Group non-top taxa as 'Others'.
154
155 - **Keep 'Not Assigned'**: Retain unassigned taxa labeled as 'Not Assigned'.
156
157 - **Normalize**: Normalize abundances to sum to 100%.
158
159 - **Remove Separation Lines**: Do not add OTU separation lines in the bars.
160
161 - **Width and Height**: Dimensions of the plot in inches (default: 10x8).
162
163 - **Device**: Output format (e.g., pdf, png, jpg, tiff).
164
165 **Outputs**
166
167 - A file containing the bar chart in the specified format.
168
169 **Usage Notes**
170
171 Ensure that the input file is a valid phyloseq object in RDS format.
172
173 **Examples**
174
175 - *Basic Bar Plot with Others and Not Assigned and with separation lines*
176
177 .. image:: $PATH_TO_IMAGES/standard_plot.png
178 :width: 515
179 :height: 395
180
181 - *Faceted Plot*
182
183 .. image:: $PATH_TO_IMAGES/facet_plot.png
184 :width: 515
185 :height: 395
186
187 - *ASV as fill input and removed separation lines*
188
189 .. image:: $PATH_TO_IMAGES/asv_fill_plot.png
190 :width: 515
191 :height: 395
192 ]]>
193 </help>
194
139 <expand macro="citations"/> 195 <expand macro="citations"/>
140 </tool> 196 </tool>