Mercurial > repos > thanhlv > merge_metaphlan_tables
comparison merge_metaphlan_tables.xml @ 0:7a090a1bd6b5 draft default tip
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
| author | thanhlv |
|---|---|
| date | Mon, 13 Feb 2023 11:37:33 +0000 |
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| -1:000000000000 | 0:7a090a1bd6b5 |
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| 1 <tool id="merge_metaphlan_tables" name="Merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> | |
| 2 <description>MetaPhlAn4 abundance tables</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="edam_ontology"/> | |
| 7 <expand macro="requirements"/> | |
| 8 <version_command>metaphlan -v</version_command> | |
| 9 <command detect_errors="aggressive"><![CDATA[ | |
| 10 merge_metaphlan_tables.py | |
| 11 #for $element in $inputs | |
| 12 '$element' | |
| 13 #end for | |
| 14 > '$output' | |
| 15 ]]> | |
| 16 </command> | |
| 17 <inputs> | |
| 18 <param name="inputs" type="data" format="tabular,txt" multiple="true" label="Predicted taxon relative abundance tables generaed by MetaPhlAn"/> | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Merged taxon relative abundance tables"/> | |
| 22 </outputs> | |
| 23 <tests> | |
| 24 <test expect_num_outputs="1"> | |
| 25 <param name="inputs" value="SRS014464-Anterior_nares-abundances.tabular,SRS014464-Anterior_nares-abundances.tabular"/> | |
| 26 <output name="output" ftype="tabular"> | |
| 27 <assert_contents> | |
| 28 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> | |
| 29 <has_text text="dataset_"/> | |
| 30 <has_text text="clade_name"/> | |
| 31 <has_line_matching expression="#.*"/> | |
| 32 </assert_contents> | |
| 33 </output> | |
| 34 </test> | |
| 35 </tests> | |
| 36 <help><![CDATA[ | |
| 37 What it does | |
| 38 ============ | |
| 39 | |
| 40 MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, | |
| 41 Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) at the species-level. | |
| 42 | |
| 43 This tool performs a table join on one or more tab-separated files with the predicted taxon relative abundances | |
| 44 that have been generated by MetaPhlAn. | |
| 45 ]]></help> | |
| 46 <expand macro="citations"/> | |
| 47 </tool> |