Mercurial > repos > iuc > metaphlan
changeset 8:1a6cdf55390f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
| author | iuc |
|---|---|
| date | Thu, 20 Apr 2023 11:26:53 +0000 |
| parents | ec368db926f4 |
| children | fd69c607b43f |
| files | macros.xml metaphlan.xml |
| diffstat | 2 files changed, 42 insertions(+), 13 deletions(-) [+] |
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--- a/macros.xml Wed Mar 29 08:00:24 2023 +0000 +++ b/macros.xml Thu Apr 20 11:26:53 2023 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">4.0.6</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">22.05</token> <!-- Metaphlan DB compatible with this version of Metaphlan v4 introduced single genome level bins (SGB) and the index syntax differs from previous versions -->
--- a/metaphlan.xml Wed Mar 29 08:00:24 2023 +0000 +++ b/metaphlan.xml Thu Apr 20 11:26:53 2023 +0000 @@ -192,16 +192,18 @@ mv 'bowtie2out' '$bowtie2out' #end if -#if $analysis.analysis_type.tax_lev.tax_lev == 'a' and $analysis.analysis_type.tax_lev.split_levels -&& -mkdir 'split_levels' -&& -python '$__tool_directory__/formatoutput.py' - split_levels - --metaphlan_output '$output_file' - --outdir 'split_levels' - $out.legacy_output +#if $analysis.analysis_type.t in ['rel_ab', 'rel_ab_w_read_stats'] + #if $analysis.analysis_type.tax_lev.tax_lev == 'a' and $analysis.analysis_type.tax_lev.split_levels + && + mkdir 'split_levels' + && + python '$__tool_directory__/formatoutput.py' + split_levels + --metaphlan_output '$output_file' + --outdir 'split_levels' + $out.legacy_output + #end if #end if #if $out.krona_output @@ -361,7 +363,7 @@ <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" /> <collection name="levels" type="list" label="${tool.name} on ${on_string}: Predicted taxon relative abundances at each taxonomic levels" > <discover_datasets pattern="(?P<designation>.+)" directory="split_levels/" format="tabular"/> - <filter>analysis['analysis_type']['tax_lev']['tax_lev'] == "a" and analysis['analysis_type']['tax_lev']['split_levels']</filter> + <filter>analysis['analysis_type']['t'] in ['rel_ab', 'rel_ab_w_read_stats'] and analysis['analysis_type']['tax_lev']['tax_lev'] == "a" and analysis['analysis_type']['tax_lev']['split_levels']</filter> </collection> <data name="krona_output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances for Krona"> <filter>out['krona_output']</filter> @@ -435,8 +437,7 @@ <not_has_text text="p__Actinobacteria"/> </assert_contents> </output> - <output_collection name="levels" type="list" > - + <output_collection name="levels" type="list"> <element name="all" ftype="tabular"> <assert_contents> <has_text text="class"/> @@ -1054,6 +1055,34 @@ </assert_contents> </output> </test> + <!-- Check a non-default analysis mode --> + <test expect_num_outputs="4"> + <section name="inputs"> + <conditional name="in"> + <param name="selector" value="raw"/> + <conditional name="raw_in"> + <param name="selector" value="single"/> + <param name="in" value="SRS014464-Anterior_nares.fasta"/> + </conditional> + </conditional> + <conditional name="db"> + <param name="db_selector" value="cached"/> + <param name="cached_db" value="test-db-20210409"/> + </conditional> + </section> + <section name="analysis"> + <conditional name="analysis_type"> + <param name="t" value="marker_ab_table"/> + </conditional> + </section> + <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-legacy-abundances.tabular" compare="sim_size"> + <assert_contents> + <has_text text="29394__H3NC06__B8A41_08715"/> + <has_text text="SampleID"/> + <has_text text="Metaphlan_Analysis"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ What it does