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comparison isoplot.xml @ 0:918940a0944c draft

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initial upload of isoplot.xml
author llegregam
date Mon, 28 Jun 2021 11:48:58 +0000
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1 <tool id='isoplot' name='Isoplot: Generate plots from isocor output' version='0.1.0'>
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'
7 #if $SP.generate_barplot:
8 -bp
9 #end if
10 #if $SP.generate_meanplot:
11 -mb
12 #end if
13 #if $SP.generate_heatmap:
14 -hm
15 #end if
16 #if $SP.generate_clustermap:
17 -cm
18 #end if
19 #if $IP.generate_barplot:
20 -IB
21 #end i
22 #if $IP.generate_meanplot:
23 -IM
24 #end if
25 #if $IP.generate_heatmap:
26 -HM
27 #end if
28 #if $stack:
29 -s
30 #end if
31 #if $verbosity:
32 -v
33 #end if
34 #if $annotation:
35 -a
36 #end if
37 -g -z '$output2' > $output1 2> '$output3'
38 ]]></command>
39 <inputs>
40 <param name='datafile' type='data' format='csv, tsv' multiple='true' label='Upload data file' />
41 <param name='template_file' type='data' format='csv, xlsx' multiple='true' label='Template file' argument='--template'/>
42 <!--param name='run_name' type='text' label='Run name' /-->
43 <param name='format' type='select' label='Plot format'>
44 <option value='pdf'>pdf</option>
45 <option value='jpeg'>jpeg</option>
46 <option value='png'>png</option>
47 <option value='svg'>svg</option>
48 <option value='html'>html</option>
49 </param>
50 <param name='value' type='select' label='Data to plot' >
51 <option value='corrected_area'>Corrected Area</option>
52 <option value='isotopologue_fraction'>Isotopologue Fraction</option>
53 <option value='mean_enrichment'>Mean Enrichment</option>
54 </param>
55 <section name='SP' title='Select static plots to generate'>
56 <param type='boolean' name='generate_barplot' label='Flag to generate barplots' argument='-bp'
57 optional='true'/>
58 <param type='boolean' name='generate_meanplot' label='Flag to generate meaned barplots' argument='-mb'
59 optional='true'/>
60 <!--<param type='boolean' name='generate_areaplot' label='Flag to generate stacked area plots'
61 argument='-sa' optional='true'/>/-->
62 <param type='boolean' name='generate_heatmap' label='Flag to generate heatmap' argument='-hm'
63 optional='true'/>
64 <param type='boolean' name='generate_clustermap' label='Flag to generate clustermap' argument='-cm'
65 optional='true'/>
66 </section>
67 <section name='IP' title='Select interactive plots to generate'>
68 <param type='boolean' name='generate_barplot' label='Flag to generate barplots' argument='-IB'
69 optional='true'/>
70 <param type='boolean' name='generate_meanplot' label='Flag to generate meaned barplots' argument='-IM'
71 optional='true'/>
72 <!-- <param type='boolean' name='generate_areaplot' label='Flag to generate stacked area plots' argument='-IS'
73 optional='true'/>-->
74 <param type='boolean' name='generate_heatmap' label='Flag to generate heatmap' argument='-HM'
75 optional='true'/>
76 </section>
77 <param type='boolean' name='stack' label='Flag to unstack bars in barplots' argument='-s' optional='true'/>
78 <param type='boolean' name='verbosity' label='Flag to get debug information' argument='-v' optional='true'/>
79 <param type='boolean' name='annotation' label='Flag to add annotations on the maps' argument='-a'
80 optional='true'/>
81 </inputs>
82 <outputs>
83 <data name='output1' format='csv' label='Formatted data used for plotting' />
84 <data name='output2' format='zip' label='Resulting plots' />
85 <data name='output3' format='txt' label='Run Info' />
86 </outputs>
87 <help><![CDATA[
88
89 Isoplot2: Plotting isotopic labelling MS data
90 =============================================
91
92 **Positional arguments:**
93
94 input_path Path to datafile
95 run_name Name of the current run
96 format Format of generated file
97
98 **optional arguments:**
99 -h, --help show this help message and exit
100 --value Choices: "corrected_area", "isotopologue_fraction", "mean_enrichment". Select values to plot. This option can be given multiple times
101
102 -m METABOLITE Metabolite(s) to plot. For all, type in 'all'
103 -c CONDITION Condition(s) to plot. For all, type in 'all'
104 -t TIME Time(s) to plot. For all, type in 'all'
105 -tp TEMPLATE_PATH Path to template file
106
107 -sa, --stacked_areaplot Create static stacked areaplot
108 -bp, --barplot Create static barplot
109 -mb, --meaned_barplot Create static barplot with meaned replicates
110
111 -IB, --interactive_barplot Create interactive stacked barplot
112 -IM, --interactive_stacked_meanplot Create interactive stacked barplot with meaned replicates
113 -IS, --interactive_areaplot Create interactive stacked areaplot
114 -hm, --static_heatmap Create a static heatmap using mean enrichment data
115 -cm, --static_clustermap Create a static heatmap with clustering using mean enrichment data
116 -HM, --interactive_heatmap Create interactive heatmap using mean enrichment data
117
118 -s, --stack Add option if barplots should be unstacked
119 -v, --verbose Turns logger to debug mode
120 -a, --annot Add option if annotations should be added on maps
121
122 ]]></help>
123 <citations>
124 <citation type='bibtex'>
125 @misc{githubisoplot,
126 author = {Le Gregam, Loic},
127 year = {2021},
128 title = {isoplot},
129 publisher = {GitHub},
130 journal = {GitHub repository},
131 url = {https://github.com/llegregam},
132 }</citation>
133 </citations>
134 </tool>