Mercurial > repos > iuc > merge_metaphlan_tables
view merge_metaphlan_tables.xml @ 14:05ad7d35ce92 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 3c1a0c4a94f78437c6df74b5348826e33e734a05
author | iuc |
---|---|
date | Mon, 29 Jul 2024 07:14:04 +0000 |
parents | 7f5d7b0e9884 |
children |
line wrap: on
line source
<tool id="merge_metaphlan_tables" name="Merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>MetaPhlAn abundance tables</description> <macros> <import>macros.xml</import> </macros> <expand macro="edam_ontology"/> <expand macro="requirements"/> <version_command>metaphlan -v</version_command> <command detect_errors="aggressive"><![CDATA[ #for $input in $inputs ln -s '$input' '${input.element_identifier}' && #end for merge_metaphlan_tables.py #for $input in $inputs '${input.element_identifier}' #end for > '$output' ]]> </command> <inputs> <param name="inputs" type="data" format="tabular,txt" multiple="true" label="Predicted taxon relative abundance tables generaed by MetaPhlAn"/> </inputs> <outputs> <data name="output" format="tabular" label="${tool.name} on ${on_string}: Merged taxon relative abundance tables"/> </outputs> <tests> <test expect_num_outputs="1"> <param name="inputs" value="SRS014464-Anterior_nares-abundances.tabular,SRS014464-Anterior_nares-abundances-samefiledifferentname.tabular"/> <output name="output" ftype="tabular"> <assert_contents> <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> <has_text text="SRS014464-Anterior_nares-abundances"/> <has_text text="SRS014464-Anterior_nares-abundances-samefiledifferentname"/> <has_text text="clade_name"/> <has_line_matching expression="#.*"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ What it does ============ MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) at the species-level. This tool performs a table join on one or more tab-separated files with the predicted taxon relative abundances that have been generated by MetaPhlAn. ]]></help> <expand macro="citations"/> </tool>