Mercurial > repos > thanhlv > merge_metaphlan_tables

diff merge_metaphlan_tables.xml @ 0:7a090a1bd6b5 draft default tip

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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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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merge_metaphlan_tables.xml	Mon Feb 13 11:37:33 2023 +0000
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+<tool id="merge_metaphlan_tables" name="Merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>MetaPhlAn4 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[
+merge_metaphlan_tables.py
+    #for $element in $inputs
+        '$element'
+    #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.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="dataset_"/>
+                    <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>