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comparison isoplot.xml @ 0:8b54f922377a draft

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"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"
author workflow4metabolomics
date Fri, 03 Sep 2021 08:01:12 +0000
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children dd3e046a72ad
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-1:000000000000 0:8b54f922377a
1 <tool id='isoplot' name='Isoplot: Generate plots from isocor output' version='1.3.0+galaxy0' profile='20.01'>
2 <requirements>
3 <requirement type='package' version='1.3.0'>isoplot</requirement>
4 </requirements>
5 <command><![CDATA[
6 isoplot '$datafile' 'galaxy' '$format' --value '$value' --template '$template_file' $SP.barplot $SP.meaned_barplot
7 $SP.static_heatmap $SP.static_clustermap $IP.interactive_barplot $IP.interactive_meanplot $IP.interactive_heatmap
8 #if $unstack:
9 -s
10 #end if
11 #if $verbosity:
12 -v
13 #end if
14 #if $annotation:
15 -a
16 #end if
17 -g -z '$plots_output' > $data_output 2> '$log_output'
18 ]]></command>
19 <inputs>
20 <param name='datafile' type='data' format='csv, tabular' multiple='true' label='Upload data that has been corrected by Isocor (.tsv format)' />
21 <param name='template_file' type='data' format='csv, xlsx' multiple='true' label='Upload template file containing plot metadata (.xlsx format)' argument='--template'/>
22 <!--param name='run_name' type='text' label='Run name' /-->
23 <param name='format' type='select' label='Plot format'>
24 <option value='pdf'>pdf</option>
25 <option value='jpeg'>jpeg</option>
26 <option value='png'>png</option>
27 <option value='svg'>svg</option>
28 <option value='html'>html</option>
29 </param>
30 <param name='value' type='select' label='Data to plot' >
31 <option value='corrected_area'>Corrected Area</option>
32 <option value='isotopologue_fraction'>Isotopologue Fraction</option>
33 <option value='mean_enrichment'>Mean Enrichment</option>
34 </param>
35 <section name='SP' title='Select static plots to generate'>
36 <param type='boolean' argument='--barplot' label='Flag to generate barplots' truevalue='-bp' falsevalue=''/>
37 <param type='boolean' argument='--meaned_barplot' label='Flag to generate meaned barplots' truevalue='-mb' falsevalue=''/>
38 <!--<param type='boolean' name='generate_areaplot' label='Flag to generate stacked area plots'
39 argument='-sa' optional='true'/>/-->
40 <param type='boolean' argument='--static_heatmap' label='Flag to generate heatmap' truevalue='-hm' falsevalue=''/>
41 <param type='boolean' argument='--static_clustermap' label='Flag to generate clustermap' truevalue='-cm' falsevalue=''/>
42 </section>
43 <section name='IP' title='Select interactive plots to generate'>
44 <param type='boolean' argument='--interactive_barplot' label='Flag to generate barplots' truevalue='-IB' falsevalue=''/>
45 <param type='boolean' argument='--interactive_meanplot' label='Flag to generate meaned barplots' truevalue='-IM' falsevalue=''/>
46 <!-- <param type='boolean' name='generate_areaplot' label='Flag to generate stacked area plots' argument='-IS'
47 optional='true'/>-->
48 <param type='boolean' argument='--interactive_heatmap' label='Flag to generate heatmap' truevalue='-HM' falsevalue=''/>
49 </section>
50 <param type='boolean' name='unstack' label='Flag to unstack bars in barplots' truevalue='-s' falsevalue=''/>
51 <param type='boolean' name='verbosity' label='Flag to get debug information' truevalue='-v' falsevalue=''/>
52 <param type='boolean' name='annotation' label='Flag to add annotations on the maps' truevalue='-a' falsevalue=''/>
53 </inputs>
54
55 <outputs>
56 <data name='data_output' format='csv' label='Formatted data used for plotting' />
57 <data name='plots_output' format='zip' label='Resulting plots' />
58 <data name='log_output' format='txt' label='Run Info' />
59 </outputs>
60
61 <tests>
62 <test>
63 <param name='datafile' value='input_data.csv' />
64 <param name='template_file' value='input_template.xlsx'/>
65 <param name='format' value='pdf' />
66 <param name='value' value='isotopologue_fraction' />
67 <section name='SP' >
68 <param name='barplot' value='true' />
69 </section>
70 <section name='IP' >
71 <param name='interactive_barplot' value='true' />
72 </section>
73 <output name='data_output' file='data_out.csv'/>
74 <output name='plots_output'>
75 <assert_contents>
76 <has_size value='2852573' delta='1000' />
77 </assert_contents>
78 </output>
79 <output name='log_output'>
80 <assert_contents>
81 <has_text text='- isoplot_log.main.cli_process - INFO - Plots created. Run is terminated' />
82 </assert_contents>
83 </output>
84 </test>
85 </tests>
86
87 <help><![CDATA[
88
89 .. class:: warningmark
90
91 We strongly encourage you to read the `documentation <https://isoplot.readthedocs.io/en/latest/>`_ before using Isoplot.
92
93 Isoplot2: Plotting isotopic labelling MS data
94 =============================================
95
96 **Positional arguments:**
97
98 input_path Path to datafile
99 run_name Name of the current run
100 format Format of generated file
101
102 **optional arguments:**
103 -h, --help show this help message and exit
104 --value Choices: "corrected_area", "isotopologue_fraction", "mean_enrichment". Select values to plot. This option can be given multiple times
105
106 -m METABOLITE Metabolite(s) to plot. For all, type in 'all'
107 -c CONDITION Condition(s) to plot. For all, type in 'all'
108 -t TIME Time(s) to plot. For all, type in 'all'
109 -tp, --template TEMPLATE_PATH Path to template file
110
111 -sa, --stacked_areaplot Create static stacked areaplot
112 -bp, --barplot Create static barplot
113 -mb, --meaned_barplot Create static barplot with meaned replicates
114
115 -IB, --interactive_barplot Create interactive stacked barplot
116 -IM, --interactive_stacked_meanplot Create interactive stacked barplot with meaned replicates
117 -IS, --interactive_areaplot Create interactive stacked areaplot
118 -hm, --static_heatmap Create a static heatmap using mean enrichment data
119 -cm, --static_clustermap Create a static heatmap with clustering using mean enrichment data
120 -HM, --interactive_heatmap Create interactive heatmap using mean enrichment data
121
122 -s, --stack Add option if barplots should be unstacked
123 -v, --verbose Turns logger to debug mode
124 -a, --annot Add option if annotations should be added on maps
125
126 ]]></help>
127 <citations>
128 <citation type='bibtex'>
129 @misc{githubisoplot,
130 author = {Le Gregam, Loic},
131 year = {2021},
132 title = {isoplot},
133 publisher = {GitHub},
134 journal = {GitHub repository},
135 url = {https://github.com/llegregam},
136 }</citation>
137 </citations>
138 </tool>