Mercurial > repos > frogs > frogs_stat
diff phyloseq_composition_macros.xml @ 0:6507a8d42a4f draft default tip
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 78ca62b54aee22893d278d9c3d495527be405f8a
| author | frogs |
|---|---|
| date | Wed, 04 Feb 2026 13:16:44 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyloseq_composition_macros.xml Wed Feb 04 13:16:44 2026 +0000 @@ -0,0 +1,66 @@ +<?xml version="1.0"?> +<macros> + <token name="@PHYLOSEQ_COMPOSITION_CMD_LINE@"> + phyloseq_composition.py + --phyloseq-rdata '$phyloseq_rdata' + --var-exp '$var_exp' + --taxa-rank-1 '$taxa_rank_1' + --taxa-set-1 '$taxa_set_1' + --taxa-rank-2 '$taxa_rank_2' + --number-of-taxa $number_of_taxa + --html '$html' + </token> + + <xml name="phyloseq_composition_inputs"> + <!-- Files --> + <param argument="--phyloseq-rdata" type="data" format="rdata" label="Phyloseq object (.Rdata)" help="Rdata file generated by the FROGS Stat 'Phyloseq Import data' tool."/> + <!-- Params --> + <param argument="--var-exp" type="text" label="Grouping variable" help="Experimental variable used to group samples (e.g., Treatment, Host type, Site, etc.)."> + <expand macro="restricted_sanitizer_validator"/> + </param> + <param argument="--taxa-rank-1" type="text" value="Kingdom" label="Taxonomic level for filtering" help="Taxonomic rank used to filter the dataset (e.g., Kingdom, Phylum, Class, Order, Family, Genus, Species)."> + <expand macro="restricted_sanitizer_validator"/> + </param> + <param argument="--taxa-set-1" type="text" value="Bacteria" label="Taxa to retain" help="Taxa to keep at the selected filtering level (e.g., Bacteria at Kingdom level, or Firmicutes at Phylum level). Multiple taxa can be specified, separated by spaces (e.g., Firmicutes Proteobacteria)."> + <expand macro="restricted_sanitizer_validator"/> + </param> + <param argument="--taxa-rank-2" type="text" value="Family" label="Taxonomic level for aggregation" help="Taxonomic rank used to aggregate data. It must be lower than the filtering level (e.g., Family when filtering at the Phylum level)."> + <expand macro="restricted_sanitizer_validator"/> + </param> + <param argument="--number-of-taxa" type="integer" value="9" min="1" label="Number of most abundant taxa to retain" help="Number of the most abundant taxa to keep (e.g., 9). All remaining taxa are grouped under 'Other'."/> + </xml> + + <!-- Test --> + <xml name="phyloseq_composition_test_input"> + <param name="phyloseq_rdata" value="references/16-phylo_import.Rdata"/> + <param name="var_exp" value="EnvType"/> + <param name="taxa_rank_1" value="Kingdom"/> + <param name="taxa_set_1" value="Bacteria"/> + <param name="taxa_rank_2" value="Phylum"/> + <param name="number_of_taxa" value="9" /> + </xml> + + <xml name="phyloseq_composition_test_output"> + <output name="html" count="1"> + <assert_contents> + <!-- HTML size or line diff can't be used as many information about path, os, date are present. --> + <!-- Here we test only title, intermediate results and output of last R command --> + <has_text text='Stat: Visualise Data Composition' /> + <has_text text='(phyloseq_composition.py' /> + <has_text text='v5.1.0)' /> + <!-- check html report contents --> + <has_text_matching expression="Phylum: Actinobacteria.*Sample: BHT0.LOT07.*Abundance: 0.3806484555" /> + <has_text_matching expression="Phylum: Bacteroidetes.*Sample: BHT0.LOT07.*Abundance: 0.0026380734" /> + <has_text_matching expression="Phylum: Cyanobacteria.*Sample: BHT0.LOT07.*Abundance: 0.0000000000" /> + <has_text_matching expression="Phylum: Firmicutes.*Sample: BHT0.LOT07.*Abundance: 0.6024168156" /> + <has_text_matching expression="Phylum: Fusobacteria.*Sample: BHT0.LOT07.*Abundance: 0.0002552974" /> + <has_text_matching expression="Phylum: Proteobacteria.*Sample: BHT0.LOT07.*Abundance: 0.0137860608" /> + <has_text_matching expression="Phylum: Spirochaetes.*Sample: BHT0.LOT07.*Abundance: 0.0000000000" /> + <has_text_matching expression="Phylum: Tenericutes.*Sample: BHT0.LOT07.*Abundance: 0.0002552974" /> + <has_text_matching expression="Phylum: Other.*Sample: BHT0.LOT07.*Abundance: 0.0000000000" /> + <has_text text='─ Session info ───────────────────────────────────────────────────────────────' /> + </assert_contents> + </output> + </xml> + +</macros>