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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/ commit 11666faa557169cc43b234ecba2a38451dec87a4
author recetox
date Thu, 01 Aug 2024 12:37:10 +0000
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-1:000000000000 0:54401f9d1a30
1 <tool id="rcx-tk" name="rcx-tk" version="0.1.0+galaxy0" python_template_version="3.5" profile="23.05">
2 <edam_topics>
3 <edam_topic>topic_3172</edam_topic>
4 <edam_topic>topic_0091</edam_topic>
5 <edam_topic>topic_3520</edam_topic>
6 </edam_topics>
7 <edam_operations>
8 <edam_operation>operation_0336</edam_operation>
9 <edam_operation>operation_3695</edam_operation>
10 </edam_operations>
11 <requirements>
12 <requirement type="package" version="0.1.0">rcx-tk</requirement>
13 </requirements>
14 <creator>
15 <person
16 givenName="Zargham"
17 familyName="Ahmad"
18 url="https://github.com/zargham-ahmad"
19 identifier="0000-0000-0000-0000"/>
20 <person
21 givenName="Kristina"
22 familyName="Gomoryova"
23 url="https://github.com/KristinaGomoryova"
24 identifier="0000-0003-4407-3917" />
25 <person
26 givenName="Helge"
27 familyName="Hecht"
28 url="https://github.com/hechth"
29 identifier="0000-0001-6744-996X" />
30 <organization
31 url="https://www.recetox.muni.cz/"
32 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
33 name="RECETOX MUNI" />
34 </creator>
35 <command><![CDATA[
36 #if $input_file.ext == "tabular"
37 #set $input_file_new = 'input.tsv'
38 #else
39 #set $input_file_new = 'input.' + str($input_file.ext)
40 #end if
41 cp ${input_file} ${input_file_new} &&
42 python3 -m rcx_tk --method ${method} ${input_file_new} 'output.tsv'
43 ]]></command>
44 <inputs>
45 <param name="input_file" type="data" format="csv,tabular,tsv,xls,xlsx,txt" label="Input data" help="Input data"/>
46 <param name="method" type="select" label="Method" help="Which data is processed: metadata or alkane file.">
47 <option value="metadata" selected="true">metadata</option>
48 <option value="alkanes">alkanes</option>
49 </param>
50 </inputs>
51 <outputs>
52 <data name="output_file" format="tabular" from_work_dir = "output.tsv" label="Processed data"/>
53 </outputs>
54 <tests>
55 <test>
56 <param name="input_file" value="input_metadata.tabular"/>
57 <param name="method" value="metadata"/>
58 <output name="output_file" file="output_metadata.tsv"/>
59 </test>
60 <test>
61 <param name="input_file" value="input_alkanes.txt"/>
62 <param name="method" value="alkanes"/>
63 <output name="output_file" file="output_alkanes.tsv"/>
64 </test>
65 </tests>
66 <help><![CDATA[
67 rcx-tk is a tool to process a metadata and/or alkane files. The main steps are columns rearrangement, validation of the file names, and derivation of new columns, such as sampleName, sequenceIdentifier, sampleIdentifier and localOrder.
68
69 On the input, a metadata or alkane file in any tabular format is expected. On the output, a tsv file is provided.
70 ]]></help>
71 <citations>
72 <citation type="doi">10.5281/zenodo.4471245</citation>
73 </citations>
74 </tool>