Mercurial > repos > iuc > merge_metaphlan_tables

comparison merge_metaphlan_tables.xml @ 3:3f05bf162005 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
author iuc
date Mon, 19 Apr 2021 20:54:50 +0000
parents 3b469e230e82
children 27250f92a01a
comparison
equal deleted inserted replaced
2:2cff76cf35c6 3:3f05bf162005
1 <tool id="merge_metaphlan_tables" name="Merge" version="@WRAPPER_VERSION@.0"> 1 <tool id="merge_metaphlan_tables" name="Merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 2 <description>MetaPhlAn abundance tables</description>
3 <description>MetaPhlAn2 files</description>
4
5 <macros> 3 <macros>
6 <import>metaphlan2_macros.xml</import> 4 <import>macros.xml</import>
7 </macros> 5 </macros>
8 6 <expand macro="edam_ontology"/>
9 <expand macro="requirements"/> 7 <expand macro="requirements"/>
10 <expand macro="stdio"/>
11
12 <version_command>merge_metaphlan_tables.py -v</version_command> 8 <version_command>merge_metaphlan_tables.py -v</version_command>
13 9 <command detect_errors="aggressive"><![CDATA[
14 <command> 10 merge_metaphlan_tables.py
15 <![CDATA[ 11 #for $element in $inputs
16 merge_metaphlan_tables.py 12 '$element'
17 #for $element in $input_files 13 #end for
18 '$element' 14 > '$output'
19 #end for
20 > '$output'
21 ]]> 15 ]]>
22 </command> 16 </command>
23
24 <inputs> 17 <inputs>
25 <param name="input_files" type="data" format="tabular,txt" multiple="True" label="MetaPhlAn2 output file to join" /> 18 <param name="inputs" type="data" format="tabular,txt" multiple="true" label="Predicted taxon relative abundance tables generaed by MetaPhlAn" />
26 </inputs> 19 </inputs>
27
28 <outputs> 20 <outputs>
29 <data format="tabular" name="output" label="${tool.name} on ${on_string}: Merged MetaPhlAn2 files" /> 21 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Merged taxon relative abundance tables" />
30 </outputs> 22 </outputs>
31
32 <tests> 23 <tests>
33 <test> 24 <test expect_num_outputs="1">
34 <param name="input_files" value="community_profile.tabular,community_profile.tabular"/> 25 <param name="inputs" value="SRS014464-Anterior_nares-abundances.tabular,SRS014464-Anterior_nares-abundances.tabular"/>
35 <output name="output"> 26 <output name="output" ftype="tabular" >
36 <assert_contents> 27 <assert_contents>
37 <has_text text="#SampleID" /> 28 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
38 <has_text text="k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron|t__Bacteroides_thetaiotaomicron_unclassified" /> 29 <has_text text="dataset_"/>
30 <has_text text="NCBI_tax_id"/>
31 <has_text text="clade_name"/>
39 </assert_contents> 32 </assert_contents>
40 </output> 33 </output>
41 </test> 34 </test>
42 </tests> 35 </tests>
36 <help><![CDATA[
37 What it does
38 ============
43 39
44 <help><![CDATA[ 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) with species-level.
45 42
46 **What it does** 43 This tool performs a table join on one or more tab-separated files with the predicted taxon relative abundances
47 44 that have been generated by MetaPhlAn.
48 MetaPhlAn is a computational tool to profile the structure and the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.
49
50 This tool performs a table join on one or more metaphlan output files
51
52 ]]></help> 45 ]]></help>
53
54 <expand macro="citations"/> 46 <expand macro="citations"/>
55 </tool> 47 </tool>