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comparison isoplot.xml @ 2:61c959ebdef5 draft default tip

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planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit b5f7f56b5ffc3c900236c077f72b321df20647be
author workflow4metabolomics
date Thu, 23 Jan 2025 15:28:29 +0000
parents dd3e046a72ad
children
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1:dd3e046a72ad 2:61c959ebdef5
1 <tool id='isoplot' name='Isoplot: Generate plots from isocor output' version='1.3.0+galaxy1' profile='20.01'> 1 <tool id='isoplot' name='Isoplot: Generate plots from isocor output' version='@TOOL_VERSION@+galaxy2' profile='20.01'>
2 <macros>
3 <token name="@TOOL_VERSION@">1.3.1</token>
4 </macros>
2 <requirements> 5 <requirements>
3 <requirement type='package' version='1.3.0'>isoplot</requirement> 6 <requirement type='package' version='3.0.3'>jinja2</requirement>
7 <requirement type='package' version='1.3.1'>zlib</requirement>
8 <requirement type='package' version='@TOOL_VERSION@'>isoplot</requirement>
4 </requirements> 9 </requirements>
5 <command><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
6 isoplot '$datafile' 'galaxy' '$format' --value '$value' --template '$template_file' $SP.barplot $SP.meaned_barplot 11 isoplot '$datafile' 'galaxy' '$format' --value '$value' --template '$template_file' --zip '$plots_output' $SP.barplot $SP.meaned_barplot
7 $SP.static_heatmap $SP.static_clustermap $IP.interactive_barplot $IP.interactive_meanplot $IP.interactive_heatmap 12 $SP.static_heatmap $SP.static_clustermap $IP.interactive_barplot $IP.interactive_meanplot $IP.interactive_heatmap
8 #if $unstack: 13 #if $unstack:
9 -s 14 -s
10 #end if 15 #end if
11 #if $verbosity: 16 #if $verbosity:
12 -v 17 -v
13 #end if 18 #end if
14 #if $annotation: 19 #if $annotation:
15 -a 20 -a
16 #end if 21 #end if
17 -g -z '$plots_output' > $data_output 2> '$log_output' 22 -g > '$data_output' 2> '$log_output'
18 ]]></command> 23 ]]></command>
19 <inputs> 24 <inputs>
20 <param name='datafile' type='data' format='csv,tabular' multiple='true' label='Upload data that has been corrected by Isocor (.tsv format)' /> 25 <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'/> 26 <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' /--> 27 <!--param name='run_name' type='text' label='Run name' /-->
57 <data name='plots_output' format='zip' label='Resulting plots' /> 62 <data name='plots_output' format='zip' label='Resulting plots' />
58 <data name='log_output' format='txt' label='Run Info' /> 63 <data name='log_output' format='txt' label='Run Info' />
59 </outputs> 64 </outputs>
60 65
61 <tests> 66 <tests>
62 <test> 67 <test expect_test_failure="true">
63 <param name='datafile' value='input_data.csv' /> 68 <param name='datafile' value='input_data.csv' />
64 <param name='template_file' value='input_template.xlsx'/> 69 <param name='template_file' value='input_template.xlsx'/>
65 <param name='format' value='pdf' /> 70 <param name='format' value='pdf' />
66 <param name='value' value='isotopologue_fraction' /> 71 <param name='value' value='isotopologue_fraction' />
67 <section name='SP' > 72 <section name='SP' >