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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
author recetox
date Tue, 21 May 2024 07:44:25 +0000
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268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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1 <tool id="rename_annotated_feature" name="Rename Annotated Feature" version="@TOOL_VERSION@+galaxy0" profile="21.09">
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2 <description>Rename columns in abundance table based on annotations table</description>
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="creator"/>
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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7 <requirements>
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8 <requirement type="package" version="2.2.1">pandas</requirement>
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9 </requirements>
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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10 <command detect_errors="exit_code"><![CDATA[
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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11 python3 '${__tool_directory__}/rename_annotated_feature.py'
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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12 --annotations_table_path '$annotations_table_path'
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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13 --abundance_table_path '$abundance_table_path'
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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14 --mode '$mode'
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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15 --output_path '$output_path'
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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16 ]]></command>
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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17 <inputs>
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18 <param name="annotations_table_path" type="data" format="tabular" label="Annotations table file" help="Path to the annotations table file."/>
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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19 <param name="abundance_table_path" type="data" format="tabular" label="Abundance table file" help="Path to the abundance table file."/>
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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20 <param name="mode" type="select" label="Mode to use for renaming" help="Can be single or multiple.">
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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21 <option value="single" selected="true">Single</option>
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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22 <option value="multiple">Multiple</option>
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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23 </param>
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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24 </inputs>
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25 <outputs>
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26 <data name="output_path" format="tabular" label="Renamed abundance table"/>
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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27 </outputs>
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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28 <tests>
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29 <test>
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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30 <param name="annotations_table_path" value="annotated_table.tsv" ftype="tabular"/>
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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31 <param name="abundance_table_path" value="abundance_table.tsv" ftype="tabular"/>
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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32 <param name="mode" value="single"/>
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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33 <output name="output_path" file="single_mode_output.tsv"/>
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34 </test>
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35 <test>
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36 <param name="annotations_table_path" value="annotated_table.tsv" ftype="tabular"/>
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37 <param name="abundance_table_path" value="abundance_table.tsv" ftype="tabular" />
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38 <param name="mode" value="multiple"/>
268fcec93d9c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
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39 <output name="output_path" file="multi_mode_output.tsv"/>
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40 </test>
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41 </tests>
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42 <help>
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43 <![CDATA[
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44 @HELP@
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45 ]]>
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46 </help>
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47 <!-- Update to the correct citation for this tool -->
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48 <citations>
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49 <citation type="doi">10.5281/zenodo.7178586</citation>
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50 <citation type="doi">10.21105/joss.02411</citation>
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51 <citation type="doi">10.1021/ac501530d</citation>
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52 </citations>
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53 </tool>