| Previous changeset 2:370b56f8a02d (2022-10-19) |
|
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5 |
|
modified:
format_metaphlan2_output.xml |
| b |
| diff -r 370b56f8a02d -r 2c87f56bd53a format_metaphlan2_output.xml --- a/format_metaphlan2_output.xml Wed Oct 19 14:39:16 2022 +0000 +++ b/format_metaphlan2_output.xml Sat Nov 04 19:00:01 2023 +0000 |
| [ |
| @@ -1,8 +1,10 @@ <tool id="format_metaphlan2_output" name="Format MetaPhlAn2" version="0.2.0"> <description>output to extract abundance at different taxonomic levels</description> - <requirements> </requirements> + <xrefs> + <xref type="bio.tools">format_metaphlan2_output</xref> + </xrefs> <stdio> </stdio> @@ -10,23 +12,21 @@ <version_command></version_command> <command><![CDATA[ - python $__tool_directory__/format_metaphlan2_output.py - --metaphlan2_output $input_file - --all_taxo_level_abundance_file $all_taxo_level_abundance_file - --kingdom_abundance_file $kingdom_abundance_file - --phylum_abundance_file $phylum_abundance_file - --class_abundance_file $class_abundance_file - --order_abundance_file $order_abundance_file - --family_abundance_file $family_abundance_file - --genus_abundance_file $genus_abundance_file - --species_abundance_file $species_abundance_file - --strains_abundance_file $strains_abundance_file + python '$__tool_directory__/format_metaphlan2_output.py' + --metaphlan2_output '$input_file' + --all_taxo_level_abundance_file '$all_taxo_level_abundance_file' + --kingdom_abundance_file '$kingdom_abundance_file' + --phylum_abundance_file '$phylum_abundance_file' + --class_abundance_file '$class_abundance_file' + --order_abundance_file '$order_abundance_file' + --family_abundance_file '$family_abundance_file' + --genus_abundance_file '$genus_abundance_file' + --species_abundance_file '$species_abundance_file' + --strains_abundance_file '$strains_abundance_file' ]]></command> - <inputs> <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)"/> </inputs> - <outputs> <data name="all_taxo_level_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Abundances for all taxonomic levels" /> <data name="kingdom_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Kingdom abundances" /> @@ -64,4 +64,4 @@ <citations> </citations> -</tool> \ No newline at end of file +</tool> |