Mercurial > repos > recetox > rcx_tk

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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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1 <tool id="rcx-tk" name="rcx-tk" version="@TOOL_VERSION@+galaxy1" profile="23.05">
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2 <description>Processes and standardizes metadata or alkane files by rearranging columns, validating file names, and deriving new columns for downstream analysis.</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.1.0</token>
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5 </macros>
0
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6 <edam_topics>
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7 <edam_topic>topic_3172</edam_topic>
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8 <edam_topic>topic_0091</edam_topic>
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9 <edam_topic>topic_3520</edam_topic>
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10 </edam_topics>
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11 <edam_operations>
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12 <edam_operation>operation_0336</edam_operation>
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13 <edam_operation>operation_3695</edam_operation>
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14 </edam_operations>
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15 <requirements>
1
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16 <requirement type="package" version="@TOOL_VERSION@">rcx-tk</requirement>
0
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17 </requirements>
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18 <creator>
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19 <person
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20 givenName="Zargham"
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21 familyName="Ahmad"
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22 url="https://github.com/zargham-ahmad"
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23 identifier="0000-0000-0000-0000"/>
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24 <person
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25 givenName="Kristina"
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26 familyName="Gomoryova"
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27 url="https://github.com/KristinaGomoryova"
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28 identifier="0000-0003-4407-3917" />
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29 <person
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30 givenName="Helge"
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31 familyName="Hecht"
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32 url="https://github.com/hechth"
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33 identifier="0000-0001-6744-996X" />
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34 <organization
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35 url="https://www.recetox.muni.cz/"
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36 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
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37 name="RECETOX MUNI" />
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38 </creator>
1
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39 <command detect_errors="aggressive"><![CDATA[
0
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40 #if $input_file.ext == "tabular"
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41 #set $input_file_new = 'input.tsv'
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42 #else
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43 #set $input_file_new = 'input.' + str($input_file.ext)
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44 #end if
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45 cp ${input_file} ${input_file_new} &&
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46 python3 -m rcx_tk --method ${method} ${input_file_new} 'output.tsv'
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47 ]]></command>
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48 <inputs>
1
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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."/>
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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.">
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51 <option value="metadata" selected="true">Metadata file</option>
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52 <option value="alkanes">Alkane file</option>
0
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53 </param>
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54 </inputs>
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55 <outputs>
1
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56 <data name="output_file" format="tabular" from_work_dir = "output.tsv" label="Processed ${method} (dataset ${input_file.id})"/>
0
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="input_file" value="input_metadata.tabular"/>
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61 <param name="method" value="metadata"/>
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62 <output name="output_file" file="output_metadata.tsv"/>
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63 </test>
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64 <test>
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65 <param name="input_file" value="input_alkanes.txt"/>
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66 <param name="method" value="alkanes"/>
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67 <output name="output_file" file="output_alkanes.tsv"/>
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68 </test>
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69 </tests>
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70 <help><![CDATA[
1
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71
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72 .. _rcx_tk:
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73
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74 ======================================
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75 rcx-tk: Metadata/Alkane File Processor
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76 ======================================
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77
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78 **Tool Description**
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79
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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.
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81
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82 How it works
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83 ------------
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84
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85 - **Column rearrangement**: Ensures columns are in the correct order for further processing.
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86 - **File name validation**: Checks that file names follow expected conventions.
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87 - **Derivation of new columns**: Automatically generates useful columns for sample tracking and analysis.
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88
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89 Inputs
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90 ------
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91
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92 1. **Input data file**
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93 Upload your sample metadata (sequence) or alkane file. Supported formats: CSV, TSV, tabular, XLS, XLSX, or TXT.
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95 2. **Processing method**
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96 Select whether to process a metadata file or an alkane file. This determines the column arrangement and validation steps.
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98 Outputs
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99 -------
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100
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101 - **Processed file**
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102 A standardized TSV file with rearranged columns and additional derived columns, ready for downstream analysis.
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103
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104 Example
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105 -------
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106
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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.
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108
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109 Notes
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110 -----
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111
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112 - Ensure your input file is correctly formatted and contains the necessary columns for your chosen processing method.
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113 - The tool supports a variety of input formats for flexibility.
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114 - The output file can be directly used in downstream data analysis workflows.
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115 ]]></help>
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116 <citations>
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117 <citation type="doi">10.5281/zenodo.4471245</citation>
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118 </citations>
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119 </tool>