Mercurial > repos > bebatut > format_metaphlan2_output

comparison format_metaphlan2_output.xml @ 3:2c87f56bd53a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sat, 04 Nov 2023 19:00:01 +0000
parents 1e74cb2c8e67
children
comparison
equal deleted inserted replaced
2:370b56f8a02d 3:2c87f56bd53a
1 <tool id="format_metaphlan2_output" name="Format MetaPhlAn2" version="0.2.0"> 1 <tool id="format_metaphlan2_output" name="Format MetaPhlAn2" version="0.2.0">
2 <description>output to extract abundance at different taxonomic levels</description> 2 <description>output to extract abundance at different taxonomic levels</description>
3
4 <requirements> 3 <requirements>
5 </requirements> 4 </requirements>
5 <xrefs>
6 <xref type="bio.tools">format_metaphlan2_output</xref>
7 </xrefs>
6 8
7 <stdio> 9 <stdio>
8 </stdio> 10 </stdio>
9 11
10 <version_command></version_command> 12 <version_command></version_command>
11 13
12 <command><![CDATA[ 14 <command><![CDATA[
13 python $__tool_directory__/format_metaphlan2_output.py 15 python '$__tool_directory__/format_metaphlan2_output.py'
14 --metaphlan2_output $input_file 16 --metaphlan2_output '$input_file'
15 --all_taxo_level_abundance_file $all_taxo_level_abundance_file 17 --all_taxo_level_abundance_file '$all_taxo_level_abundance_file'
16 --kingdom_abundance_file $kingdom_abundance_file 18 --kingdom_abundance_file '$kingdom_abundance_file'
17 --phylum_abundance_file $phylum_abundance_file 19 --phylum_abundance_file '$phylum_abundance_file'
18 --class_abundance_file $class_abundance_file 20 --class_abundance_file '$class_abundance_file'
19 --order_abundance_file $order_abundance_file 21 --order_abundance_file '$order_abundance_file'
20 --family_abundance_file $family_abundance_file 22 --family_abundance_file '$family_abundance_file'
21 --genus_abundance_file $genus_abundance_file 23 --genus_abundance_file '$genus_abundance_file'
22 --species_abundance_file $species_abundance_file 24 --species_abundance_file '$species_abundance_file'
23 --strains_abundance_file $strains_abundance_file 25 --strains_abundance_file '$strains_abundance_file'
24 ]]></command> 26 ]]></command>
25
26 <inputs> 27 <inputs>
27 <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="Output file of MetaPhlAN with all taxonomic levels (from kingdom to strains, --metaphlan2_output)"/> 28 <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="Output file of MetaPhlAN with all taxonomic levels (from kingdom to strains, --metaphlan2_output)"/>
28 </inputs> 29 </inputs>
29
30 <outputs> 30 <outputs>
31 <data name="all_taxo_level_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Abundances for all taxonomic levels" /> 31 <data name="all_taxo_level_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Abundances for all taxonomic levels" />
32 <data name="kingdom_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Kingdom abundances" /> 32 <data name="kingdom_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Kingdom abundances" />
33 <data name="phylum_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Phylum abundances" /> 33 <data name="phylum_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Phylum abundances" />
34 <data name="class_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Class abundances" /> 34 <data name="class_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Class abundances" />