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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/ commit 48dbee053949c9e18cf965805b0115320d05af3c
author recetox
date Mon, 19 May 2025 11:03:48 +0000
parents 54401f9d1a30
children
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0:54401f9d1a30 1:9b4b624c4d60
1 <tool id="rcx-tk" name="rcx-tk" version="0.1.0+galaxy0" python_template_version="3.5" profile="23.05"> 1 <tool id="rcx-tk" name="rcx-tk" version="@TOOL_VERSION@+galaxy1" profile="23.05">
2 <description>Processes and standardizes metadata or alkane files by rearranging columns, validating file names, and deriving new columns for downstream analysis.</description>
3 <macros>
4 <token name="@TOOL_VERSION@">0.1.0</token>
5 </macros>
2 <edam_topics> 6 <edam_topics>
3 <edam_topic>topic_3172</edam_topic> 7 <edam_topic>topic_3172</edam_topic>
4 <edam_topic>topic_0091</edam_topic> 8 <edam_topic>topic_0091</edam_topic>
5 <edam_topic>topic_3520</edam_topic> 9 <edam_topic>topic_3520</edam_topic>
6 </edam_topics> 10 </edam_topics>
7 <edam_operations> 11 <edam_operations>
8 <edam_operation>operation_0336</edam_operation> 12 <edam_operation>operation_0336</edam_operation>
9 <edam_operation>operation_3695</edam_operation> 13 <edam_operation>operation_3695</edam_operation>
10 </edam_operations> 14 </edam_operations>
11 <requirements> 15 <requirements>
12 <requirement type="package" version="0.1.0">rcx-tk</requirement> 16 <requirement type="package" version="@TOOL_VERSION@">rcx-tk</requirement>
13 </requirements> 17 </requirements>
14 <creator> 18 <creator>
15 <person 19 <person
16 givenName="Zargham" 20 givenName="Zargham"
17 familyName="Ahmad" 21 familyName="Ahmad"
30 <organization 34 <organization
31 url="https://www.recetox.muni.cz/" 35 url="https://www.recetox.muni.cz/"
32 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" 36 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
33 name="RECETOX MUNI" /> 37 name="RECETOX MUNI" />
34 </creator> 38 </creator>
35 <command><![CDATA[ 39 <command detect_errors="aggressive"><![CDATA[
36 #if $input_file.ext == "tabular" 40 #if $input_file.ext == "tabular"
37 #set $input_file_new = 'input.tsv' 41 #set $input_file_new = 'input.tsv'
38 #else 42 #else
39 #set $input_file_new = 'input.' + str($input_file.ext) 43 #set $input_file_new = 'input.' + str($input_file.ext)
40 #end if 44 #end if
41 cp ${input_file} ${input_file_new} && 45 cp ${input_file} ${input_file_new} &&
42 python3 -m rcx_tk --method ${method} ${input_file_new} 'output.tsv' 46 python3 -m rcx_tk --method ${method} ${input_file_new} 'output.tsv'
43 ]]></command> 47 ]]></command>
44 <inputs> 48 <inputs>
45 <param name="input_file" type="data" format="csv,tabular,tsv,xls,xlsx,txt" label="Input data" help="Input data"/> 49 <param name="input_file" type="data" format="csv,tabular,tsv,xls,xlsx,txt" label="Input data file" help="Upload your sample metadata (sequence) or alkane file."/>
46 <param name="method" type="select" label="Method" help="Which data is processed: metadata or alkane file."> 50 <param name="method" type="select" label="Processing method" help="Select whether to process a metadata file or an alkane file. This determines the column arrangement and validation steps.">
47 <option value="metadata" selected="true">metadata</option> 51 <option value="metadata" selected="true">Metadata file</option>
48 <option value="alkanes">alkanes</option> 52 <option value="alkanes">Alkane file</option>
49 </param> 53 </param>
50 </inputs> 54 </inputs>
51 <outputs> 55 <outputs>
52 <data name="output_file" format="tabular" from_work_dir = "output.tsv" label="Processed data"/> 56 <data name="output_file" format="tabular" from_work_dir = "output.tsv" label="Processed ${method} (dataset ${input_file.id})"/>
53 </outputs> 57 </outputs>
54 <tests> 58 <tests>
55 <test> 59 <test>
56 <param name="input_file" value="input_metadata.tabular"/> 60 <param name="input_file" value="input_metadata.tabular"/>
57 <param name="method" value="metadata"/> 61 <param name="method" value="metadata"/>
62 <param name="method" value="alkanes"/> 66 <param name="method" value="alkanes"/>
63 <output name="output_file" file="output_alkanes.tsv"/> 67 <output name="output_file" file="output_alkanes.tsv"/>
64 </test> 68 </test>
65 </tests> 69 </tests>
66 <help><![CDATA[ 70 <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 71
69 On the input, a metadata or alkane file in any tabular format is expected. On the output, a tsv file is provided. 72 .. _rcx_tk:
73
74 ======================================
75 rcx-tk: Metadata/Alkane File Processor
76 ======================================
77
78 **Tool Description**
79
80 rcx-tk is a tool for processing sample metadata (sequence) and alkane files. It standardizes your input by rearranging columns, validating file names, and deriving new columns such as `sampleName`, `sequenceIdentifier`, `sampleIdentifier`, and `localOrder`. This ensures your data is ready for downstream analysis and compatible with standardized workflows.
81
82 How it works
83 ------------
84
85 - **Column rearrangement**: Ensures columns are in the correct order for further processing.
86 - **File name validation**: Checks that file names follow expected conventions.
87 - **Derivation of new columns**: Automatically generates useful columns for sample tracking and analysis.
88
89 Inputs
90 ------
91
92 1. **Input data file**
93 Upload your sample metadata (sequence) or alkane file. Supported formats: CSV, TSV, tabular, XLS, XLSX, or TXT.
94
95 2. **Processing method**
96 Select whether to process a metadata file or an alkane file. This determines the column arrangement and validation steps.
97
98 Outputs
99 -------
100
101 - **Processed file**
102 A standardized TSV file with rearranged columns and additional derived columns, ready for downstream analysis.
103
104 Example
105 -------
106
107 Suppose you have a metadata file in CSV or tabular format. Select "Metadata file" as the processing method and upload your file. The tool will output a processed TSV file with standardized columns and additional identifiers.
108
109 Notes
110 -----
111
112 - Ensure your input file is correctly formatted and contains the necessary columns for your chosen processing method.
113 - The tool supports a variety of input formats for flexibility.
114 - The output file can be directly used in downstream data analysis workflows.
70 ]]></help> 115 ]]></help>
71 <citations> 116 <citations>
72 <citation type="doi">10.5281/zenodo.4471245</citation> 117 <citation type="doi">10.5281/zenodo.4471245</citation>
73 </citations> 118 </citations>
74 </tool> 119 </tool>