Mercurial > repos > iuc > orthofinder_onlygroups
changeset 10:b6ec80429d54 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 3753e5e77bcc883c92e06ae1d5bcb21eab150f35
| author | iuc |
|---|---|
| date | Mon, 11 Aug 2025 11:42:12 +0000 |
| parents | b3d25fae5389 |
| children | |
| files | macros.xml orthofinder_only_groups.xml |
| diffstat | 2 files changed, 232 insertions(+), 99 deletions(-) [+] |
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--- a/macros.xml Mon Jan 15 10:18:14 2024 +0000 +++ b/macros.xml Mon Aug 11 11:42:12 2025 +0000 @@ -1,11 +1,52 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">2.5.5</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> + <token name="@PROFILE@">24.0</token> <xml name="citations"> <citations> <citation type="doi">10.1186/s13059-015-0721-2</citation> </citations> </xml> + <xml name="output_selector_minimal"> + <param name="output_selector" type="select" optional="false" multiple="true" label="Outputs"> + <yield/> + <!-- Comparative_Genomics_Statistics --> + <option value="specs_overlap" selected="true">Species overlaps</option> + <option value="stat_overall" selected="true">Statistics Overall</option> + <option value="stat_specs" selected="true">Statistics per Species</option> + <!-- Orthogroups results (deprecated) --> + <option value="orthogroups">Orthogroups (deprecated)</option> + <option value="orthogroups_legacy">Orthogroups - legacy format (deprecated)</option> + <option value="orthogroups_unassigned_genes">Orthogroups - with unassigned genes (deprecated)</option> + + </param> + </xml> + + <xml name="output_selector_full"> + <expand macro="output_selector_minimal"> + <option value="phylogenetic_hierarchical_orthogroups" selected="true">Phylogenetic Hierarchical Orthogroups Directory</option> + <!-- Orthologues results --> + <option value="orthologues" selected="true">Orthologs</option> + <option value="orthologues_per_species">Orthologs per species</option> + <!-- gene trees --> + <option value="gene_trees" selected="true">Gene Trees</option> + <option value="resolved_gene_trees">Resolved Gene Trees</option> + <!-- Species Trees Directory --> + <option value="species_tree" selected="true">Species Tree</option> + <option value="species_tree_node_labels" selected="true">Species Trees with nodes labels</option> + <!-- Gene_Duplication_Events --> + <option value="speciestree_gene_duplication_0.5_support">Species tree with gene duplications (support>=0.5)</option> + <option value="duplications">Duplications</option> + <!-- Comparative_Genomics_Statistics --> + <option value="duplications_per_orthogroup">Duplications per Orthogroup</option> + <option value="duplications_per_species_tree_node">Duplications per Species Tree Node</option> + <option value="orthologuesstats_many_to_many">OrthologuesStats many-to-many</option> + <option value="orthologuesstats_one_to_many">OrthologuesStats one-to-many</option> + <option value="orthologuesstats_many_to_one">OrthologuesStats many-to-one</option> + <option value="orthologuesstats_total" selected="true">OrthologuesStats Total</option> + </expand> + </xml> + </macros>
--- a/orthofinder_only_groups.xml Mon Jan 15 10:18:14 2024 +0000 +++ b/orthofinder_only_groups.xml Mon Aug 11 11:42:12 2025 +0000 @@ -1,4 +1,4 @@ -<tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> +<tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>finds orthogroups in a set of proteomes</description> <macros> <import>macros.xml</import> @@ -116,13 +116,11 @@ <param name="seqIDs" type="data" format="txt" label="Select the SequencesIds file" help="SequencesIDs.txt file from the blast output files of a previous OrthoFinder run."/> </when> </conditional> - <conditional name="trees"> <param name="run_mode" type="select" label="Orthofinder run mode"> <option value="full" selected="true">Full run (including gene trees)</option> <option value="-og">Stop after inferring orthogroups (no gene trees)</option> </param> - <when value="full"> <conditional name="tree_method"> <param name="method" type="select" label="Method for gene tree inference"> @@ -145,69 +143,126 @@ <when value="dendroblast"/> </conditional> + <expand macro="output_selector_full"/> </when> - - <when value="-og"/> + <when value="-og"> + <expand macro="output_selector_minimal"/> + </when> </conditional> - <param argument="-I" name="inflation" type="float" value="1.5" label="Inflation parameter" help="Modify inflation parameter for MCL. Not recommended." /> - <param name="output_duplications" type="boolean" checked="false" label="Generate output about gene duplication events"/> </inputs> <outputs> - <!-- Orthogroups results --> - <data format="txt" name="orthogroups1" label="OrthoFinder on ${on_string}: orthogroups (txt)" from_work_dir="results/Orthogroups/Orthogroups.txt" /> - <data format="tsv" name="orthogroups2" label="OrthoFinder on ${on_string}: orthogroups (tsv)" from_work_dir="results/Orthogroups/Orthogroups.tsv" /> - <data format="tsv" name="hogs" label="OrthoFinder on ${on_string}: hierarchical orthogroups (tsv)" from_work_dir="results/Phylogenetic_Hierarchical_Orthogroups/N0.tsv" > + <collection name="hogs" type="list" label="${tool.name} on ${on_string}: hierarchical orthogroups (tsv)"> + <discover_datasets pattern="__name_and_ext__" directory="results/Phylogenetic_Hierarchical_Orthogroups/" /> + <filter>trees['run_mode'] == "full"</filter> + <filter>"phylogenetic_hierarchical_orthogroups" in trees['output_selector']</filter> + </collection> + + <!-- Orthologues results --> + <collection name="orthologues" type="list:list" label="${tool.name} on ${on_string}: Orthologues (tsv)"> + <discover_datasets pattern="Orthologues_(?P<identifier_0>.+)/(?P<identifier_1>.+)\.tsv" directory="results/Orthologues/" match_relative_path="true" format="tsv" recurse="true"/> + <filter>trees['run_mode'] == "full"</filter> + <filter>"orthologues" in trees['output_selector']</filter> + </collection> + <collection name="orthologues_per_species" type="list" label="${tool.name} on ${on_string}: Orthologues per species(tsv)"> + <discover_datasets pattern="(?P<designation>.+)\.tsv" directory="results/Orthologues/" format="tsv"/> + <filter>trees['run_mode'] == "full"</filter> + <filter>"orthologues_per_species" in trees['output_selector']</filter> + </collection> + + <!-- Orthogroups results (deprecated) --> + <data format="txt" name="orthogroups1" label="${tool.name} on ${on_string}: orthogroups (txt)" from_work_dir="results/Orthogroups/Orthogroups.txt"> + <filter>"orthogroups" in trees['output_selector']</filter> + </data> + <data format="tsv" name="orthogroups2" label="${tool.name} on ${on_string}: orthogroups (tsv)" from_work_dir="results/Orthogroups/Orthogroups.tsv"> + <filter>"orthogroups_legacy" in trees['output_selector']</filter> + </data> + <data format="tsv" name="unassigned_genes" label="${tool.name} on ${on_string}: unassigned genes" from_work_dir="results/Orthogroups/Orthogroups_UnassignedGenes.tsv"> + <filter>"orthogroups_unassigned_genes" in trees['output_selector']</filter> + </data> + + <!-- gene trees --> + <collection name="genetrees" type="list" label="${tool.name} on ${on_string}: gene trees"> + <discover_datasets pattern="(?P<designation>.+)\.txt" directory="results/Gene_Trees" format="newick" /> + <filter>trees['run_mode'] == "full"</filter> + <filter>"gene_trees" in trees['output_selector']</filter> + </collection> + <collection name="resolved_genetrees" type="list" label="${tool.name} on ${on_string}: resolved gene trees"> + <discover_datasets pattern="(?P<designation>.+)\.txt" directory="results/Resolved_Gene_Trees" format="newick" /> + <filter>trees['run_mode'] == "full"</filter> + <filter>"resolved_gene_trees" in trees['output_selector']</filter> + </collection> + + <!-- Species Trees Directory --> + <data format="newick" name="species_tree" label="${tool.name} on ${on_string}: species tree" from_work_dir="results/Species_Tree/SpeciesTree_rooted.txt"> + <filter>trees['run_mode'] == "full"</filter> + <filter>"species_tree" in trees['output_selector']</filter> + </data> + <data format="newick" name="species_tree_label" label="${tool.name} on ${on_string}: species tree with node labels" from_work_dir="results/Species_Tree/SpeciesTree_rooted_node_labels.txt"> <filter>trees['run_mode'] == "full"</filter> + <filter>"species_tree_node_labels" in trees['output_selector']</filter> </data> - <data format="tsv" name="specs_overlap" label="OrthoFinder on ${on_string}: species overlaps" from_work_dir="results/Comparative_Genomics_Statistics/Orthogroups_SpeciesOverlaps.tsv" /> - <data format="tsv" name="unassigned_genes" label="OrthoFinder on ${on_string}: unassigned genes" from_work_dir="results/Orthogroups/Orthogroups_UnassignedGenes.tsv" /> - <data format="tsv" name="stat_overall" label="OrthoFinder on ${on_string}: overall comparative genomics statistics" from_work_dir="results/Comparative_Genomics_Statistics/Statistics_Overall.tsv" /> - <data format="tsv" name="stat_specs" label="OrthoFinder on ${on_string}: per species comparative genomics statistics" from_work_dir="results/Comparative_Genomics_Statistics/Statistics_PerSpecies.tsv" /> + + <!-- Comparative Genomics Statistics Directory --> + <data format="tsv" name="duplications_per_orthogroup" label="${tool.name} on ${on_string}: duplications per orthogroup" from_work_dir="results/Comparative_Genomics_Statistics/Duplications_per_Orthogroup.tsv"> + <filter>trees['run_mode'] == "full"</filter> + <filter>"duplications_per_orthogroup" in trees['output_selector']</filter> + </data> + <data format="tsv" name="duplications_per_species_tree_node" label="${tool.name} on ${on_string}: duplications per species tree node" from_work_dir="results/Comparative_Genomics_Statistics/Duplications_per_Species_Tree_Node.tsv"> + <filter>trees['run_mode'] == "full"</filter> + <filter>"duplications_per_species_tree_node" in trees['output_selector']</filter> + </data> + <data format="tsv" name="specs_overlap" label="${tool.name} on ${on_string}: species overlaps" from_work_dir="results/Comparative_Genomics_Statistics/Orthogroups_SpeciesOverlaps.tsv"> + <filter>"specs_overlap" in trees['output_selector']</filter> + </data> + <data format="tsv" name="orthologuesstats_many_to_many" label="${tool.name} on ${on_string}: OrthologuesStats many-to-many" from_work_dir="results/Comparative_Genomics_Statistics/OrthologuesStats_many-to-many.tsv"> + <filter>trees['run_mode'] == "full"</filter> + <filter>"orthologuesstats_many_to_many" in trees['output_selector']</filter> + </data> + <data format="tsv" name="orthologuesstats_one_to_many" label="${tool.name} on ${on_string}: OrthologuesStats one-to-many" from_work_dir="results/Comparative_Genomics_Statistics/OrthologuesStats_one-to-many.tsv"> + <filter>trees['run_mode'] == "full"</filter> + <filter>"orthologuesstats_one_to_many" in trees['output_selector']</filter> + </data> + <data format="tsv" name="orthologuesstats_many_to_one" label="${tool.name} on ${on_string}: OrthologuesStats many-to-one" from_work_dir="results/Comparative_Genomics_Statistics/OrthologuesStats_many-to-one"> + <filter>trees['run_mode'] == "full"</filter> + <filter>"orthologuesstats_many_to_one" in trees['output_selector']</filter> + </data> + <data format="tsv" name="orthologuesstats_total" label="${tool.name} on ${on_string}: OrthologuesStats Total" from_work_dir="results/Comparative_Genomics_Statistics/OrthologuesStats_Total.tsv"> + <filter>trees['run_mode'] == "full"</filter> + <filter>"orthologuesstats_total" in trees['output_selector']</filter> + </data> + <data format="tsv" name="stat_overall" label="${tool.name} on ${on_string}: overall comparative genomics statistics" from_work_dir="results/Comparative_Genomics_Statistics/Statistics_Overall.tsv"> + <filter>"stat_overall" in trees['output_selector']</filter> + </data> + <data format="tsv" name="stat_specs" label="${tool.name} on ${on_string}: per species comparative genomics statistics" from_work_dir="results/Comparative_Genomics_Statistics/Statistics_PerSpecies.tsv"> + <filter>"stat_specs" in trees['output_selector']</filter> + </data> + + <!-- Gene_Duplication_Events --> + <data format="newick" name="species_tree_duplications" label="${tool.name} on ${on_string}: species tree with duplication events" from_work_dir="results/Gene_Duplication_Events/SpeciesTree_Gene_Duplications_0.5_Support.txt"> + <filter>trees['run_mode'] == "full"</filter> + <filter>"speciestree_gene_duplication_0.5_support" in trees['output_selector']</filter> + </data> + <data format="tsv" name="duplications" label="${tool.name} on ${on_string}: duplication events" from_work_dir="results/Gene_Duplication_Events/Duplications.tsv"> + <filter>trees['run_mode'] == "full"</filter> + <filter>"duplications" in trees['output_selector']</filter> + </data> <!-- working directory : blast outputs--> - <collection name="wdblast" type="list" label="OrthoFinder on ${on_string}: blast outputs"> + <collection name="wdblast" type="list" label="${tool.name} on ${on_string}: blast outputs"> <discover_datasets pattern="__name_and_ext__" directory="results/WorkingDirectory/blast" /> <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter> </collection> - <collection name="wdfasta" type="list" label="OrthoFinder on ${on_string}: fasta from blast" > + <collection name="wdfasta" type="list" label="${tool.name} on ${on_string}: fasta from blast" > <discover_datasets pattern="(?P<designation>.+)\.fa" directory="results/WorkingDirectory/fa" format="fasta" /> <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter> </collection> - <data format="txt" name="SpeciesIDs" label="OrthoFinder on ${on_string}: SpeciesIDs" from_work_dir="results/WorkingDirectory/SpeciesIDs.txt" > - <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter> - </data> - <data format="txt" name="SequenceIDs" label="OrthoFinder on ${on_string}: SequencesIDs" from_work_dir="results/WorkingDirectory/SequenceIDs.txt" > + <data format="txt" name="SpeciesIDs" label="${tool.name} on ${on_string}: SpeciesIDs" from_work_dir="results/WorkingDirectory/SpeciesIDs.txt" > <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter> </data> - - <data format="newick" name="species_tree" label="OrthoFinder on ${on_string}: species tree" from_work_dir="results/Species_Tree/SpeciesTree_rooted.txt"> - <filter>trees['run_mode'] == "full"</filter> - </data> - <data format="newick" name="species_tree_label" label="OrthoFinder on ${on_string}: species tree with node labels" from_work_dir="results/Species_Tree/SpeciesTree_rooted_node_labels.txt"> - <filter>trees['run_mode'] == "full"</filter> + <data format="txt" name="SequenceIDs" label="${tool.name} on ${on_string}: SequencesIDs" from_work_dir="results/WorkingDirectory/SequenceIDs.txt" > + <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter> </data> - <collection name="genetrees" type="list" label="OrthoFinder on ${on_string}: gene trees"> - <discover_datasets pattern="(?P<designation>.+)\.txt" directory="results/Gene_Trees" format="newick" /> - <filter>trees['run_mode'] == "full"</filter> - </collection> - - <data format="newick" name="species_tree_duplications" label="OrthoFinder on ${on_string}: species tree with duplication events" from_work_dir="results/Gene_Duplication_Events/SpeciesTree_Gene_Duplications_0.5_Support.txt"> - <filter>trees['run_mode'] == "full" and output_duplications</filter> - </data> - <data format="tsv" name="duplications" label="OrthoFinder on ${on_string}: duplication events" from_work_dir="results/Gene_Duplication_Events/Duplications.tsv"> - <filter>trees['run_mode'] == "full" and output_duplications</filter> - </data> - <data format="tsv" name="duplications_per_orthogroup" label="OrthoFinder on ${on_string}: duplications per orthogroup" from_work_dir="results/Comparative_Genomics_Statistics/Duplications_per_Orthogroup.tsv"> - <filter>trees['run_mode'] == "full" and output_duplications</filter> - </data> - <data format="tsv" name="duplications_per_species_tree_node" label="OrthoFinder on ${on_string}: duplications per species tree node" from_work_dir="results/Comparative_Genomics_Statistics/Duplications_per_Species_Tree_Node.tsv"> - <filter>trees['run_mode'] == "full" and output_duplications</filter> - </data> - <collection name="resolved_trees" type="list" label="OrthoFinder on ${on_string}: resolved gene trees"> - <discover_datasets pattern="(?P<designation>.+)\.txt" directory="results/Resolved_Gene_Trees" format="newick" /> - <filter>trees['run_mode'] == "full" and output_duplications</filter> - </collection> </outputs> <tests> <!-- no trees + diamond + input files have no extension fasta/faa/fa --> @@ -221,6 +276,7 @@ </conditional> <conditional name="trees"> <param name="run_mode" value="-og" /> + <param name="output_selector" value="orthogroups,orthogroups_legacy,orthogroups_unassigned_genes,specs_overlap,stat_overall,stat_specs"/> </conditional> <param name="inflation" value="1.5" /> <output name="specs_overlap"> @@ -279,6 +335,7 @@ </conditional> <conditional name="trees"> <param name="run_mode" value="-og" /> + <param name="output_selector" value="orthogroups,orthogroups_legacy,orthogroups_unassigned_genes,specs_overlap,stat_overall,stat_specs"/> </conditional> <param name="inflation" value="1.5" /> <output name="specs_overlap"> @@ -338,6 +395,7 @@ </conditional> <conditional name="trees"> <param name="run_mode" value="-og" /> + <param name="output_selector" value="orthogroups,orthogroups_legacy,orthogroups_unassigned_genes,specs_overlap,stat_overall,stat_specs"/> </conditional> <param name="inflation" value="1.5" /> <output name="specs_overlap"> @@ -400,6 +458,7 @@ </conditional> <conditional name="trees"> <param name="run_mode" value="-og" /> + <param name="output_selector" value="orthogroups,orthogroups_legacy,orthogroups_unassigned_genes,specs_overlap,stat_overall,stat_specs"/> </conditional> <param name="inflation" value="1.5" /> <output name="specs_overlap"> @@ -484,17 +543,18 @@ </conditional> <conditional name="trees"> <param name="run_mode" value="-og" /> + <param name="output_selector" value="orthogroups,orthogroups_legacy,orthogroups_unassigned_genes,specs_overlap,stat_overall,stat_specs"/> </conditional> <param name="inflation" value="1.5" /> <output name="orthogroups1" value="results_fromblast/Orthogroups.txt"/> <output name="orthogroups2" value="results_fromblast/Orthogroups.tsv"/> + <output name="unassigned_genes" value="results_fromblast/Orthogroups_UnassignedGenes.tsv"/> <output name="specs_overlap" value="results_fromblast/Orthogroups_SpeciesOverlaps.tsv"/> - <output name="unassigned_genes" value="results_fromblast/Orthogroups_UnassignedGenes.tsv"/> <output name="stat_overall" value="results_fromblast/Statistics_Overall.tsv" lines_diff="2"/> <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.tsv"/> </test> <!-- full mode + diamond + input files have extension fasta/faa/fa --> - <test expect_num_outputs="10"> + <test expect_num_outputs="11"> <conditional name="init"> <param name="start" value="fasta" /> <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" /> @@ -504,6 +564,7 @@ </conditional> <conditional name="trees"> <param name="run_mode" value="full" /> + <param name="output_selector" value="phylogenetic_hierarchical_orthogroups,orthogroups,orthogroups_legacy,orthogroups_unassigned_genes,gene_trees,resolved_gene_trees,specs_overlap,stat_overall,stat_specs,species_tree,species_tree_node_labels"/> </conditional> <param name="inflation" value="1.5" /> <output name="specs_overlap"> @@ -551,19 +612,22 @@ </assert_contents> </output> <output name="species_tree" value="results/SpeciesTree_rooted.txt" compare="sim_size"/> - <output_collection name="genetrees" type="list" count="0"/> - <output name="hogs"> - <assert_contents> - <has_text text="HOG" /> - <has_text text="OG" /> - <has_text text="Gene Tree Parent Clade" /> - <has_text text="Mycoplasma_agalactiae"/> - <has_text text="Mycoplasma_gallisepticum"/> - <has_text text="Mycoplasma_genitalium"/> - <has_text text="Mycoplasma_hyopneumoniae"/> - <has_n_columns n="7"/> - </assert_contents> - </output> + <output_collection name="genetrees" type="list" count="325"/> + <output_collection name="resolved_genetrees" type="list" count="325"/> + <output_collection name="hogs" type="list" count="3"> + <element name="N0"> + <assert_contents> + <has_text text="HOG" /> + <has_text text="OG" /> + <has_text text="Gene Tree Parent Clade" /> + <has_text text="Mycoplasma_agalactiae"/> + <has_text text="Mycoplasma_gallisepticum"/> + <has_text text="Mycoplasma_genitalium"/> + <has_text text="Mycoplasma_hyopneumoniae"/> + <has_n_columns n="7"/> + </assert_contents> + </element> + </output_collection> </test> <!-- full mode + diamond + input files have extension fasta/faa/fa + duplications --> <test expect_num_outputs="15"> @@ -576,9 +640,9 @@ </conditional> <conditional name="trees"> <param name="run_mode" value="full" /> + <param name="output_selector" value="phylogenetic_hierarchical_orthogroups,orthogroups,orthogroups_legacy,orthogroups_unassigned_genes,gene_trees,resolved_gene_trees,duplications_per_orthogroup,duplications_per_species_tree_node,specs_overlap,stat_overall,stat_specs,species_tree,species_tree_node_labels,speciestree_gene_duplication_0.5_support,duplications"/> </conditional> <param name="inflation" value="1.5" /> - <param name="output_duplications" value="true" /> <output name="specs_overlap"> <assert_contents> <has_text text="Mycoplasma_agalactiae"/> @@ -629,21 +693,23 @@ <output name="duplications_per_orthogroup" value="results/Duplications_per_Orthogroup.tsv" compare="sim_size"/> <output name="duplications_per_species_tree_node" value="results/Duplications_per_Species_Tree_Node.tsv" compare="sim_size"/> <output_collection name="genetrees" type="list" count="325"/> - <output_collection name="resolved_trees" type="list" count="325"/> - <output name="hogs"> - <assert_contents> - <has_text text="HOG" /> - <has_text text="OG" /> - <has_text text="Gene Tree Parent Clade" /> - <has_text text="Mycoplasma_agalactiae"/> - <has_text text="Mycoplasma_gallisepticum"/> - <has_text text="Mycoplasma_genitalium"/> - <has_text text="Mycoplasma_hyopneumoniae"/> - <has_n_columns n="7"/> - </assert_contents> - </output> + <output_collection name="resolved_genetrees" type="list" count="325"/> + <output_collection name="hogs" type="list" count="3"> + <element name="N0"> + <assert_contents> + <has_text text="HOG" /> + <has_text text="OG" /> + <has_text text="Gene Tree Parent Clade" /> + <has_text text="Mycoplasma_agalactiae"/> + <has_text text="Mycoplasma_gallisepticum"/> + <has_text text="Mycoplasma_genitalium"/> + <has_text text="Mycoplasma_hyopneumoniae"/> + <has_n_columns n="7"/> + </assert_contents> + </element> + </output_collection> </test> - <!-- trees + diamond + input files have no extension fasta/faa/fa + msa --> + <!-- diamond + input files have no extension fasta/faa/fa + msa --> <test expect_num_outputs="6"> <conditional name="init"> <param name="start" value="fasta" /> @@ -654,11 +720,7 @@ </conditional> <conditional name="trees"> <param name="run_mode" value="-og" /> - <conditional name="tree_method"> - <param name="method" value="msa" /> - <param name="msa_program" value="muscle" /> - <param name="msa_tree_program" value="raxml" /> - </conditional> + <param name="output_selector" value="orthogroups,orthogroups_legacy,orthogroups_unassigned_genes,specs_overlap,stat_overall,stat_specs"/> </conditional> <param name="inflation" value="1.5" /> <output name="specs_overlap"> @@ -707,7 +769,7 @@ </output> </test> <!-- trees + diamond + input files have no extension fasta/faa/fa + msa --> - <test expect_num_outputs="10"> + <test expect_num_outputs="12"> <conditional name="init"> <param name="start" value="fasta" /> <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" /> @@ -722,6 +784,7 @@ <param name="msa_program" value="muscle" /> <param name="msa_tree_program" value="raxml" /> </conditional> + <param name="output_selector" value="phylogenetic_hierarchical_orthogroups,orthologues,orthologues_per_species,orthogroups,orthogroups_legacy,orthogroups_unassigned_genes,gene_trees,specs_overlap,stat_overall,stat_specs,species_tree,species_tree_node_labels"/> </conditional> <param name="inflation" value="1.5" /> <output name="specs_overlap"> @@ -768,18 +831,48 @@ <has_n_columns n="5"/> </assert_contents> </output> - <output name="hogs"> - <assert_contents> - <has_text text="HOG" /> - <has_text text="OG" /> - <has_text text="Gene Tree Parent Clade" /> - <has_text text="Mycoplasma_agalactiae"/> - <has_text text="Mycoplasma_gallisepticum"/> - <has_text text="Mycoplasma_genitalium"/> - <has_text text="Mycoplasma_hyopneumoniae"/> - <has_n_columns n="7"/> - </assert_contents> - </output> + <output_collection name="hogs" type="list" count="3"> + <element name="N0"> + <assert_contents> + <has_text text="HOG" /> + <has_text text="OG" /> + <has_text text="Gene Tree Parent Clade" /> + <has_text text="Mycoplasma_agalactiae"/> + <has_text text="Mycoplasma_gallisepticum"/> + <has_text text="Mycoplasma_genitalium"/> + <has_text text="Mycoplasma_hyopneumoniae"/> + <has_n_columns n="7"/> + </assert_contents> + </element> + </output_collection> + <output_collection name="orthologues" type="list:list" count="4"> + <element name="Mycoplasma_agalactiae.faa" count="3"> + <element name="Mycoplasma_agalactiae.faa__v__Mycoplasma_gallisepticum.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element> + <element name="Mycoplasma_agalactiae.faa__v__Mycoplasma_genitalium.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element> + <element name="Mycoplasma_agalactiae.faa__v__Mycoplasma_hyopneumoniae.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element> + </element> + <element name="Mycoplasma_gallisepticum.faa" count="3"> + <element name="Mycoplasma_gallisepticum.faa__v__Mycoplasma_agalactiae.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element> + <element name="Mycoplasma_gallisepticum.faa__v__Mycoplasma_genitalium.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element> + <element name="Mycoplasma_gallisepticum.faa__v__Mycoplasma_hyopneumoniae.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element> + </element> + <element name="Mycoplasma_genitalium.faa" count="3"> + <element name="Mycoplasma_genitalium.faa__v__Mycoplasma_agalactiae.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element> + <element name="Mycoplasma_genitalium.faa__v__Mycoplasma_gallisepticum.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element> + <element name="Mycoplasma_genitalium.faa__v__Mycoplasma_hyopneumoniae.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element> + </element> + <element name="Mycoplasma_hyopneumoniae.faa" count="3"> + <element name="Mycoplasma_hyopneumoniae.faa__v__Mycoplasma_agalactiae.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element> + <element name="Mycoplasma_hyopneumoniae.faa__v__Mycoplasma_gallisepticum.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element> + <element name="Mycoplasma_hyopneumoniae.faa__v__Mycoplasma_genitalium.faa"><assert_contents><has_n_columns n="3"/></assert_contents></element> + </element> + </output_collection> + <output_collection name="orthologues_per_species" type="list" count="4"> + <element name="Mycoplasma_agalactiae.faa"><assert_contents><has_n_columns n="4"/></assert_contents></element> + <element name="Mycoplasma_gallisepticum.faa"><assert_contents><has_n_columns n="4"/></assert_contents></element> + <element name="Mycoplasma_genitalium.faa"><assert_contents><has_n_columns n="4"/></assert_contents></element> + <element name="Mycoplasma_hyopneumoniae.faa"><assert_contents><has_n_columns n="4"/></assert_contents></element> + </output_collection> <assert_command> <has_text text="-M 'msa'"/> <has_text text="-A 'muscle'"/> @@ -792,8 +885,7 @@ OrthoFinder OnlyGroups ====================== -Full readme at https://github.com/davidemms/OrthoFinder/blob/master/README.md -Summary sketch at https://github.com/davidemms/OrthoFinder/blob/master/OrthoFinder-manual.pdf +More information at https://orthofinder.github.io/OrthoFinder/ OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format (Emms, D.M. and Kelly, S., 2015).