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comparison gaiac_boxplot/gaiac_boxplot.xml @ 0:0763bb545f98 draft

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planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty
author jay
date Thu, 15 May 2025 14:44:13 +0000
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1 <tool id="gaiac_box_plot" name="GAIAC Box Plot" version="0.1.0" python_template_version="3.10" >
2 <description>Generates box plots for numerical data columns in a dataset</description>
3 <requirements>
4 <requirement type="package" version="2.2.3">pandas</requirement>
5 <requirement type="package" version="3.10.0">matplotlib</requirement>
6 <requirement type="package" version="0.13.2">seaborn</requirement>
7 </requirements>
8
9 <stdio>
10 <exit_code range="1" level="fatal" />
11 </stdio>
12 <command detect_errors="exit_code"><![CDATA[
13 python '$__tool_directory__/boxplot.py' --infile '$infile' -C '$clm_list_y' -H '$fig_height' -W '$fig_width' -T '$plottitile' -O 'out.png' --ylab '$clm_lab_y' --xlab '$clm_lab_x'
14
15 #if $Sel_x_tick_labels.Plot == 'advance'
16 --custom_xtick_name '$Sel_x_tick_labels.label'
17 #end if
18 ]]></command>
19
20 <inputs>
21 <param name="infile" type="data" format="tabular" label="Input file" />
22 <param name="plottitile" type="text" value="Box Plot" label="Plot title" />
23 <param name="fig_height" type="text" value="3" label="Figure Height" />
24 <param name="fig_width" type="text" value="5" label="Figure Width" />
25 <param name="clm_lab_y" type="text" value="" size="30" label="Label for y axis"/>
26 <param name="clm_lab_x" type="text" value="" size="30" label="Label for x axis"/>
27 <param name="clm_list_y" label="Select columns for y axis" type="data_column" data_ref="infile" numerical="True" multiple="true" use_header_names="true">
28 <validator type="no_options" message="Please select atleast one column."/>
29 </param>
30
31 <conditional name='Sel_x_tick_labels' >
32 <param name="Plot" type="select" label="label for legend" argument="" help="Data plotting method">
33 <option value="advance" > Advance option for custom labels for X tick labels</option>
34 <option value="default" selected="true"> Default labels</option>
35 </param>
36
37 <when value="advance">
38 <param name="label" type="text" value="" label="label for X tick as text" help="A list that gives custom labels for legends as comma seperated text"/>
39 </when>
40
41 <when value="default">
42 </when>
43 </conditional>
44 </inputs>
45
46 <outputs>
47 <data name='output1' format='png' label="Output" from_work_dir="out.png" ></data>
48 </outputs>
49
50 <tests>
51 <test>
52 <!-- Input file and plot parameters -->
53 <param name="infile" value="test.tsv"/>
54 <param name="plottitile" value="Box Plot"/>
55 <param name="fig_height" value="5"/>
56 <param name="fig_width" value="7"/>
57 <param name="clm_lab_y" value="Values"/>
58 <param name="clm_lab_x" value="Categories"/>
59 <!-- Select the column for the Y axis -->
60 <param name="clm_list_y" value="1"/>
61 <!-- Use default for custom X tick labels -->
62 <param name="Sel_x_tick_labels|Plot" value="default"/>
63 <!-- Output file -->
64 <output name="output1" file="out.png" />
65 </test>
66 </tests>
67
68 <help><![CDATA[
69 .. class:: infomark
70
71 **What it does**
72
73 This tool generates boxplot for the selected columns (parameters) from the dataset
74
75 -----
76
77 **Inputs**
78 Boxplot
79 * **--infile** Input files
80 * **--column_list_y** List of columns
81 * **--custom_xtick_name** xtick label
82 * **--output** Output file
83 * **--title** Figure title
84 * **--height** Figure height
85 * **--width** Figure width
86 * **--ylab** Y labels
87 * **--xlab** X labels
88
89 -----
90
91
92 **Outputs**
93 * Returns png file with the boxplot]]></help>
94
95 <citations>
96 <citation type="bibtex">
97
98
99 @article{dubey2022,
100 title={AirPiuG-Galaxy software platform based open-source GUI tools for data collection and analysis from low cost air pollution sensors},
101 author={Dubey, R and Joshi, J and Patra, A and Blankenberg, D},
102 journal={GitHub repository},
103 url = {https://github.com/ravishdubey/OPCN3API},
104 year={2022},
105 publisher={GitHub}
106 }
107
108 </citation>
109
110 </citations>
111 </tool>