Mercurial > repos > iuc > merge_metaphlan_tables

comparison merge_metaphlan_tables.xml @ 12:7f5d7b0e9884 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 70ba929dd55348ee43753e6ae29bd45c5cdf5471
author iuc
date Sat, 10 Feb 2024 23:56:53 +0000
parents e073891b2afc
children
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equal deleted inserted replaced
11:0270541aaf46 12:7f5d7b0e9884
5 </macros> 5 </macros>
6 <expand macro="edam_ontology"/> 6 <expand macro="edam_ontology"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <version_command>metaphlan -v</version_command> 8 <version_command>metaphlan -v</version_command>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 merge_metaphlan_tables.py 10 #for $input in $inputs
11 #for $element in $inputs 11 ln -s '$input' '${input.element_identifier}' &&
12 '$element' 12 #end for
13
14 merge_metaphlan_tables.py
15 #for $input in $inputs
16 '${input.element_identifier}'
13 #end for 17 #end for
14 > '$output' 18 > '$output'
15 ]]> 19 ]]>
16 </command> 20 </command>
17 <inputs> 21 <inputs>
20 <outputs> 24 <outputs>
21 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Merged taxon relative abundance tables"/> 25 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Merged taxon relative abundance tables"/>
22 </outputs> 26 </outputs>
23 <tests> 27 <tests>
24 <test expect_num_outputs="1"> 28 <test expect_num_outputs="1">
25 <param name="inputs" value="SRS014464-Anterior_nares-abundances.tabular,SRS014464-Anterior_nares-abundances.tabular"/> 29 <param name="inputs" value="SRS014464-Anterior_nares-abundances.tabular,SRS014464-Anterior_nares-abundances-samefiledifferentname.tabular"/>
26 <output name="output" ftype="tabular"> 30 <output name="output" ftype="tabular">
27 <assert_contents> 31 <assert_contents>
28 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 32 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
29 <has_text text="dataset_"/> 33 <has_text text="SRS014464-Anterior_nares-abundances"/>
34 <has_text text="SRS014464-Anterior_nares-abundances-samefiledifferentname"/>
30 <has_text text="clade_name"/> 35 <has_text text="clade_name"/>
31 <has_line_matching expression="#.*"/> 36 <has_line_matching expression="#.*"/>
32 </assert_contents> 37 </assert_contents>
33 </output> 38 </output>
34 </test> 39 </test>