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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 179e3fd2aeb66484e49e6370e9507e24d118f4ea
| author | iuc |
|---|---|
| date | Mon, 15 Jan 2024 10:18:14 +0000 |
| parents | 3b974afde673 |
| children |
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<tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>finds orthogroups in a set of proteomes</description> <macros> <import>macros.xml</import> </macros> <xrefs> <xref type="bio.tools">OrthoFinder</xref> </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">orthofinder</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #import re ## prepare inputs #if $init.start == "fasta": #set $infiles = "" #for $input in $init.input_fasta #set $identifier=re.sub('[^\w\-\s\.]', '_', str($input.element_identifier)) ln -s '$input' '${identifier}.fasta' && #set $infiles = $infiles + str($identifier) + "," #end for #set $infiles = $infiles[:-1] #elif $init.start == "blast": #set $infilesbl = "" #for $input in $init.input_blast_out #set $identifier=re.sub('[^\w\-\s\.]', '_', str($input.element_identifier)) ln -s '$input' '$identifier' && #set $infilesbl = $infilesbl + str($identifier) + "," #end for #set $infilesbl = $infilesbl[:-1] #set $infilesfa = "" #for $input in $init.input_blast_fa #set $identifier=re.sub('[^\w\-\s\.]', '_', str($input.element_identifier)) ln -s '$input' '$identifier' && #set $infilesfa = $infilesfa + str($identifier) + "," #end for #set $infilesfa = $infilesfa[:-1] #set $identifier=re.sub('[^\w\-\s\.]', '_', str($init.specIDs.element_identifier)) ln -s $init.specIDs $identifier && #set $identifier=re.sub('[^\w\-\s\.]', '_', str($init.seqIDs.element_identifier)) ln -s $init.seqIDs $identifier && #end if ## start Orthofinder orthofinder #if $init.start == "fasta": -f . -S $init.search.search_program $init.input_type #elif $init.start == "blast": -b . #end if -I $inflation #if $trees.run_mode == "full": -M '${trees.tree_method.method}' #if $trees.tree_method.method == "msa": -A '${trees.tree_method.msa_program}' -T '${trees.tree_method.msa_tree_program}' #end if #else: $trees.run_mode #end if -t \${GALAXY_SLOTS:-1} -a \${GALAXY_SLOTS:-1} && mv OrthoFinder/Results_* results #if $init.start == "fasta": #if $init.search.search_program == "blast": #if $init.search.keepblastout: && mkdir -p results/WorkingDirectory/blast results/WorkingDirectory/fa && mv results/WorkingDirectory/Blast* results/WorkingDirectory/blast/ && mv results/WorkingDirectory/*.fa results/WorkingDirectory/fa/ #end if #end if #end if ]]></command> <inputs> <!-- Control where Orthofinder starts --> <conditional name="init"> <param name="start" type="select" label="Orthofinder starting point" help="OrthoFinder can be run in 2 steps. Choose 'From fasta files' to run OrthoFinder from scratch or 'From blast results' if you have all the blast results from a previous OrthoFinder run."> <option value="fasta" selected="true">From fasta files</option> <option value="blast">From blast results</option> </param> <when value="fasta"> <param name="input_fasta" type="data" format="fasta" multiple="true" label="Select input fasta files" help="One fasta file per species; species and sequence names in the results will remain the same than in the input files."/> <param name="input_type" type="select" label="Input contains nucleotide or amino acid sequences?"> <option value="">Amino acid</option> <option value="-d">Nucleotide</option> </param> <conditional name="search"> <param name="search_program" type="select" label="Sequence search program"> <option value="diamond" selected="true">Diamond (faster)</option> <option value="diamond_ultra_sens">Diamond ultra-sensitive</option> <option value="blast">Blast</option> <option value="blast_gz">Blast_gz - blast results gzipped</option> </param> <when value="blast"> <param name="keepblastout" type="boolean" checked="true" label="Do you want to get the blast results?" help="Used to re-run OrthoFinder from pre-computed blast results"/> </when> <when value="diamond"></when> <when value="diamond_ultra_sens"></when> <when value="blast_gz"></when> </conditional> </when> <when value="blast"> <param name="input_blast_out" type="data_collection" collection_type="list" format="txt" label="Select the pre-computed blast files" help="blastX_Y.txt files from the blast output files of a previous OrthoFinder run." /> <param name="input_blast_fa" type="data_collection" collection_type="list" format="fasta" label="Select the fasta files" help="= SpeciesX.fa files from the blast output files of a previous OrthoFinder run." /> <param name="specIDs" type="data" format="txt" label="Select the SpeciesIds file" help="SpeciesIDs.txt file from the blast output files of a previous OrthoFinder run."/> <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"> <option value="dendroblast" selected="true">Dendroblast (faster)</option> <option value="msa">MSA (Multiple Sequence Aligments)</option> </param> <when value="msa"> <param name="msa_program" type="select" label="MSA program"> <option value="mafft" selected="true">Mafft</option> <option value="muscle">Muscle</option> </param> <param name="msa_tree_program" type="select" label="Tree inference method"> <option value="fasttree" selected="true">FastTree (recommended)</option> <option value="raxml">raxml</option> <option value="raxml-ng">raxml-ng</option> <option value="iqtree">iqtree</option> </param> </when> <when value="dendroblast"/> </conditional> </when> <when value="-og"/> </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" > <filter>trees['run_mode'] == "full"</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" /> <!-- working directory : blast outputs--> <collection name="wdblast" type="list" label="OrthoFinder 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" > <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" > <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> <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 --> <test expect_num_outputs="6"> <conditional name="init"> <param name="start" value="fasta" /> <param name="input_fasta" ftype="fasta" value="inputs/no_fa_ext/AcAcaud_trinity,inputs/no_fa_ext/AmAmphi_trinity,inputs/no_fa_ext/ApApomp_trinity,inputs/no_fa_ext/AsAsp1_trinity" /> <conditional name="search"> <param name="search_program" value="diamond"/> </conditional> </conditional> <conditional name="trees"> <param name="run_mode" value="-og" /> </conditional> <param name="inflation" value="1.5" /> <output name="specs_overlap"> <assert_contents> <has_text text="AcAcaud_trinity"/> <has_text text="AmAmphi_trinity"/> <has_text text="ApApomp_trinity"/> <has_text text="AsAsp1_trinity"/> <has_n_columns n="5"/> </assert_contents> </output> <output name="unassigned_genes"> <assert_contents> <has_text text="AcAcaud_trinity"/> <has_text text="AmAmphi_trinity"/> <has_text text="ApApomp_trinity"/> <has_text text="AsAsp1_trinity"/> <has_n_columns n="5"/> </assert_contents> </output> <output name="stat_overall"> <assert_contents> <has_text text="Number of genes in orthogroups"/> <has_text text="Number of unassigned genes"/> <has_text text="Percentage of orthogroups"/> <has_text text="Number of orthogroups"/> <has_text text="Number of genes"/> <has_text text="G50 (assigned genes)"/> <has_text text="G50 (all genes)"/> <has_text text="O50 (assigned genes)"/> <has_text text="O50 (all genes)"/> </assert_contents> </output> <output name="stat_specs"> <assert_contents> <has_text text="AcAcaud_trinity"/> <has_text text="AmAmphi_trinity"/> <has_text text="ApApomp_trinity"/> <has_text text="AsAsp1_trinity"/> <has_text text="Number of genes per-species in orthogroup"/> <has_text text="Percentage of orthogroups"/> <has_text text="Number of orthogroups"/> <has_text text="Number of genes"/> <has_n_columns n="5"/> </assert_contents> </output> </test> <!-- no trees + diamond + input files have extension fasta/faa/fa --> <test expect_num_outputs="6"> <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" /> <conditional name="search"> <param name="search_program" value="diamond"/> </conditional> </conditional> <conditional name="trees"> <param name="run_mode" value="-og" /> </conditional> <param name="inflation" value="1.5" /> <output name="specs_overlap"> <assert_contents> <has_text text="Mycoplasma_agalactiae"/> <has_text text="Mycoplasma_gallisepticum"/> <has_text text="Mycoplasma_genitalium"/> <has_text text="Mycoplasma_hyopneumoniae"/> <has_n_columns n="5"/> </assert_contents> </output> <output name="unassigned_genes"> <assert_contents> <has_text text="Mycoplasma_agalactiae"/> <has_text text="Mycoplasma_gallisepticum"/> <has_text text="Mycoplasma_genitalium"/> <has_text text="Mycoplasma_hyopneumoniae"/> <has_n_columns n="5"/> </assert_contents> </output> <output name="stat_overall"> <assert_contents> <has_text text="Number of genes in orthogroups"/> <has_text text="Number of unassigned genes"/> <has_text text="Percentage of orthogroups"/> <has_text text="Number of orthogroups"/> <has_text text="Number of genes"/> <has_text text="G50 (assigned genes)"/> <has_text text="G50 (all genes)"/> <has_text text="O50 (assigned genes)"/> <has_text text="O50 (all genes)"/> </assert_contents> </output> <output name="stat_specs"> <assert_contents> <has_text text="Mycoplasma_agalactiae"/> <has_text text="Mycoplasma_gallisepticum"/> <has_text text="Mycoplasma_genitalium"/> <has_text text="Mycoplasma_hyopneumoniae"/> <has_text text="Number of genes per-species in orthogroup"/> <has_text text="Percentage of orthogroups"/> <has_text text="Number of orthogroups"/> <has_text text="Number of genes"/> <has_n_columns n="5"/> </assert_contents> </output> </test> <!-- no trees + diamond + input files have extension fasta/faa/fa + keep blast out --> <test expect_num_outputs="10"> <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" /> <conditional name="search"> <param name="search_program" value="blast"/> <param name="keepblastout" value="true" /> </conditional> </conditional> <conditional name="trees"> <param name="run_mode" value="-og" /> </conditional> <param name="inflation" value="1.5" /> <output name="specs_overlap"> <assert_contents> <has_text text="Mycoplasma_agalactiae"/> <has_text text="Mycoplasma_gallisepticum"/> <has_text text="Mycoplasma_genitalium"/> <has_text text="Mycoplasma_hyopneumoniae"/> <has_n_columns n="5"/> </assert_contents> </output> <output name="unassigned_genes"> <assert_contents> <has_text text="Mycoplasma_agalactiae"/> <has_text text="Mycoplasma_gallisepticum"/> <has_text text="Mycoplasma_genitalium"/> <has_text text="Mycoplasma_hyopneumoniae"/> <has_n_columns n="5"/> </assert_contents> </output> <output name="stat_overall"> <assert_contents> <has_text text="Number of genes in orthogroups"/> <has_text text="Number of unassigned genes"/> <has_text text="Percentage of orthogroups"/> <has_text text="Number of orthogroups"/> <has_text text="Number of genes"/> <has_text text="G50 (assigned genes)"/> <has_text text="G50 (all genes)"/> <has_text text="O50 (assigned genes)"/> <has_text text="O50 (all genes)"/> </assert_contents> </output> <output name="stat_specs"> <assert_contents> <has_text text="Mycoplasma_agalactiae"/> <has_text text="Mycoplasma_gallisepticum"/> <has_text text="Mycoplasma_genitalium"/> <has_text text="Mycoplasma_hyopneumoniae"/> <has_text text="Number of genes per-species in orthogroup"/> <has_text text="Percentage of orthogroups"/> <has_text text="Number of orthogroups"/> <has_text text="Number of genes"/> <has_n_columns n="5"/> </assert_contents> </output> <output name="SequenceIDs" value="inputs/blastids/SequenceIDs.txt" /> <output_collection name="wdfasta" type="list" count="4"/> <output_collection name="wdblast" type="list" count="16"/> </test> <!-- no trees + blast + input files have extension fasta/faa/fa--> <test expect_num_outputs="6"> <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" /> <conditional name="search"> <param name="search_program" value="blast"/> <param name="keepblastout" value="false" /> </conditional> </conditional> <conditional name="trees"> <param name="run_mode" value="-og" /> </conditional> <param name="inflation" value="1.5" /> <output name="specs_overlap"> <assert_contents> <has_text text="Mycoplasma_agalactiae"/> <has_text text="Mycoplasma_gallisepticum"/> <has_text text="Mycoplasma_genitalium"/> <has_text text="Mycoplasma_hyopneumoniae"/> <has_n_columns n="5"/> </assert_contents> </output> <output name="unassigned_genes"> <assert_contents> <has_text text="Mycoplasma_agalactiae"/> <has_text text="Mycoplasma_gallisepticum"/> <has_text text="Mycoplasma_genitalium"/> <has_text text="Mycoplasma_hyopneumoniae"/> <has_n_columns n="5"/> </assert_contents> </output> <output name="stat_overall"> <assert_contents> <has_text text="Number of genes in orthogroups"/> <has_text text="Number of unassigned genes"/> <has_text text="Percentage of orthogroups"/> <has_text text="Number of orthogroups"/> <has_text text="Number of genes"/> <has_text text="G50 (assigned genes)"/> <has_text text="G50 (all genes)"/> <has_text text="O50 (assigned genes)"/> <has_text text="O50 (all genes)"/> </assert_contents> </output> <output name="stat_specs"> <assert_contents> <has_text text="Mycoplasma_agalactiae"/> <has_text text="Mycoplasma_gallisepticum"/> <has_text text="Mycoplasma_genitalium"/> <has_text text="Mycoplasma_hyopneumoniae"/> <has_text text="Number of genes per-species in orthogroup"/> <has_text text="Percentage of orthogroups"/> <has_text text="Number of orthogroups"/> <has_text text="Number of genes"/> <has_n_columns n="5"/> </assert_contents> </output> </test> <!-- no trees + uploaded blast--> <test expect_num_outputs="6"> <conditional name="init"> <param name="start" value="blast" /> <param name="input_blast_out"> <collection type="list"> <element name="Blast0_0.txt" value="inputs/blastout/Blast0_0.txt"/> <element name="Blast0_1.txt" value="inputs/blastout/Blast0_1.txt"/> <element name="Blast0_2.txt" value="inputs/blastout/Blast0_2.txt"/> <element name="Blast0_3.txt" value="inputs/blastout/Blast0_3.txt"/> <element name="Blast1_0.txt" value="inputs/blastout/Blast1_0.txt"/> <element name="Blast1_1.txt" value="inputs/blastout/Blast1_1.txt"/> <element name="Blast1_2.txt" value="inputs/blastout/Blast1_2.txt"/> <element name="Blast1_3.txt" value="inputs/blastout/Blast1_3.txt"/> <element name="Blast2_0.txt" value="inputs/blastout/Blast2_0.txt"/> <element name="Blast2_1.txt" value="inputs/blastout/Blast2_1.txt"/> <element name="Blast2_2.txt" value="inputs/blastout/Blast2_2.txt"/> <element name="Blast2_3.txt" value="inputs/blastout/Blast2_3.txt"/> <element name="Blast3_0.txt" value="inputs/blastout/Blast3_0.txt"/> <element name="Blast3_1.txt" value="inputs/blastout/Blast3_1.txt"/> <element name="Blast3_2.txt" value="inputs/blastout/Blast3_2.txt"/> <element name="Blast3_3.txt" value="inputs/blastout/Blast3_3.txt"/> </collection> </param> <param name="input_blast_fa"> <collection type="list"> <element name="Species0.fa" value="inputs/blastfa/Species0.fa"/> <element name="Species1.fa" value="inputs/blastfa/Species1.fa"/> <element name="Species2.fa" value="inputs/blastfa/Species2.fa"/> <element name="Species3.fa" value="inputs/blastfa/Species3.fa"/> </collection> </param> <param name="specIDs" ftype="txt" value="inputs/blastids/SpeciesIDs.txt"/> <param name="seqIDs" ftype="txt" value="inputs/blastids/SequenceIDs.txt"/> </conditional> <conditional name="trees"> <param name="run_mode" value="-og" /> </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="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"> <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" /> <conditional name="search"> <param name="search_program" value="diamond"/> </conditional> </conditional> <conditional name="trees"> <param name="run_mode" value="full" /> </conditional> <param name="inflation" value="1.5" /> <output name="specs_overlap"> <assert_contents> <has_text text="Mycoplasma_agalactiae"/> <has_text text="Mycoplasma_gallisepticum"/> <has_text text="Mycoplasma_genitalium"/> <has_text text="Mycoplasma_hyopneumoniae"/> <has_n_columns n="5"/> </assert_contents> </output> <output name="unassigned_genes"> <assert_contents> <has_text text="Mycoplasma_agalactiae"/> <has_text text="Mycoplasma_gallisepticum"/> <has_text text="Mycoplasma_genitalium"/> <has_text text="Mycoplasma_hyopneumoniae"/> <has_n_columns n="5"/> </assert_contents> </output> <output name="stat_overall"> <assert_contents> <has_text text="Number of genes in orthogroups"/> <has_text text="Number of unassigned genes"/> <has_text text="Percentage of orthogroups"/> <has_text text="Number of orthogroups"/> <has_text text="Number of genes"/> <has_text text="G50 (assigned genes)"/> <has_text text="G50 (all genes)"/> <has_text text="O50 (assigned genes)"/> <has_text text="O50 (all genes)"/> </assert_contents> </output> <output name="stat_specs"> <assert_contents> <has_text text="Mycoplasma_agalactiae"/> <has_text text="Mycoplasma_gallisepticum"/> <has_text text="Mycoplasma_genitalium"/> <has_text text="Mycoplasma_hyopneumoniae"/> <has_text text="Number of genes per-species in orthogroup"/> <has_text text="Percentage of orthogroups"/> <has_text text="Number of orthogroups"/> <has_text text="Number of genes"/> <has_n_columns n="5"/> </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> </test> <!-- full mode + diamond + input files have extension fasta/faa/fa + duplications --> <test expect_num_outputs="15"> <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" /> <conditional name="search"> <param name="search_program" value="diamond"/> </conditional> </conditional> <conditional name="trees"> <param name="run_mode" value="full" /> </conditional> <param name="inflation" value="1.5" /> <param name="output_duplications" value="true" /> <output name="specs_overlap"> <assert_contents> <has_text text="Mycoplasma_agalactiae"/> <has_text text="Mycoplasma_gallisepticum"/> <has_text text="Mycoplasma_genitalium"/> <has_text text="Mycoplasma_hyopneumoniae"/> <has_n_columns n="5"/> </assert_contents> </output> <output name="unassigned_genes"> <assert_contents> <has_text text="Mycoplasma_agalactiae"/> <has_text text="Mycoplasma_gallisepticum"/> <has_text text="Mycoplasma_genitalium"/> <has_text text="Mycoplasma_hyopneumoniae"/> <has_n_columns n="5"/> </assert_contents> </output> <output name="stat_overall"> <assert_contents> <has_text text="Number of genes in orthogroups"/> <has_text text="Number of unassigned genes"/> <has_text text="Percentage of orthogroups"/> <has_text text="Number of orthogroups"/> <has_text text="Number of genes"/> <has_text text="G50 (assigned genes)"/> <has_text text="G50 (all genes)"/> <has_text text="O50 (assigned genes)"/> <has_text text="O50 (all genes)"/> </assert_contents> </output> <output name="stat_specs"> <assert_contents> <has_text text="Mycoplasma_agalactiae"/> <has_text text="Mycoplasma_gallisepticum"/> <has_text text="Mycoplasma_genitalium"/> <has_text text="Mycoplasma_hyopneumoniae"/> <has_text text="Number of genes per-species in orthogroup"/> <has_text text="Percentage of orthogroups"/> <has_text text="Number of orthogroups"/> <has_text text="Number of genes"/> <has_n_columns n="5"/> </assert_contents> </output> <output name="species_tree" value="results/SpeciesTree_rooted.txt" compare="sim_size"/> <output name="species_tree_duplications" value="results/SpeciesTree_Gene_Duplications_0.5_Support.txt" compare="sim_size"/> <output name="duplications" value="results/Duplications.tsv" compare="sim_size"/> <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> </test> <!-- trees + diamond + input files have no extension fasta/faa/fa + msa --> <test expect_num_outputs="6"> <conditional name="init"> <param name="start" value="fasta" /> <param name="input_fasta" ftype="fasta" value="inputs/no_fa_ext/AcAcaud_trinity,inputs/no_fa_ext/AmAmphi_trinity,inputs/no_fa_ext/ApApomp_trinity,inputs/no_fa_ext/AsAsp1_trinity" /> <conditional name="search"> <param name="search_program" value="diamond"/> </conditional> </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> </conditional> <param name="inflation" value="1.5" /> <output name="specs_overlap"> <assert_contents> <has_text text="AcAcaud_trinity"/> <has_text text="AmAmphi_trinity"/> <has_text text="ApApomp_trinity"/> <has_text text="AsAsp1_trinity"/> <has_n_columns n="5"/> </assert_contents> </output> <output name="unassigned_genes"> <assert_contents> <has_text text="AcAcaud_trinity"/> <has_text text="AmAmphi_trinity"/> <has_text text="ApApomp_trinity"/> <has_text text="AsAsp1_trinity"/> <has_n_columns n="5"/> </assert_contents> </output> <output name="stat_overall"> <assert_contents> <has_text text="Number of genes in orthogroups"/> <has_text text="Number of unassigned genes"/> <has_text text="Percentage of orthogroups"/> <has_text text="Number of orthogroups"/> <has_text text="Number of genes"/> <has_text text="G50 (assigned genes)"/> <has_text text="G50 (all genes)"/> <has_text text="O50 (assigned genes)"/> <has_text text="O50 (all genes)"/> </assert_contents> </output> <output name="stat_specs"> <assert_contents> <has_text text="AcAcaud_trinity"/> <has_text text="AmAmphi_trinity"/> <has_text text="ApApomp_trinity"/> <has_text text="AsAsp1_trinity"/> <has_text text="Number of genes per-species in orthogroup"/> <has_text text="Percentage of orthogroups"/> <has_text text="Number of orthogroups"/> <has_text text="Number of genes"/> <has_n_columns n="5"/> </assert_contents> </output> </test> <!-- trees + diamond + input files have no extension fasta/faa/fa + msa --> <test expect_num_outputs="10"> <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" /> <conditional name="search"> <param name="search_program" value="diamond"/> </conditional> </conditional> <conditional name="trees"> <param name="run_mode" value="full" /> <conditional name="tree_method"> <param name="method" value="msa" /> <param name="msa_program" value="muscle" /> <param name="msa_tree_program" value="raxml" /> </conditional> </conditional> <param name="inflation" value="1.5" /> <output name="specs_overlap"> <assert_contents> <has_text text="Mycoplasma_agalactiae"/> <has_text text="Mycoplasma_gallisepticum"/> <has_text text="Mycoplasma_genitalium"/> <has_text text="Mycoplasma_hyopneumoniae"/> <has_n_columns n="5"/> </assert_contents> </output> <output name="unassigned_genes"> <assert_contents> <has_text text="Mycoplasma_agalactiae"/> <has_text text="Mycoplasma_gallisepticum"/> <has_text text="Mycoplasma_genitalium"/> <has_text text="Mycoplasma_hyopneumoniae"/> <has_n_columns n="5"/> </assert_contents> </output> <output name="stat_overall"> <assert_contents> <has_text text="Number of genes in orthogroups"/> <has_text text="Number of unassigned genes"/> <has_text text="Percentage of orthogroups"/> <has_text text="Number of orthogroups"/> <has_text text="Number of genes"/> <has_text text="G50 (assigned genes)"/> <has_text text="G50 (all genes)"/> <has_text text="O50 (assigned genes)"/> <has_text text="O50 (all genes)"/> </assert_contents> </output> <output name="stat_specs"> <assert_contents> <has_text text="Mycoplasma_agalactiae"/> <has_text text="Mycoplasma_gallisepticum"/> <has_text text="Mycoplasma_genitalium"/> <has_text text="Mycoplasma_hyopneumoniae"/> <has_text text="Number of genes per-species in orthogroup"/> <has_text text="Percentage of orthogroups"/> <has_text text="Number of orthogroups"/> <has_text text="Number of genes"/> <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> <assert_command> <has_text text="-M 'msa'"/> <has_text text="-A 'muscle'"/> <has_text text="-T 'raxml'"/> </assert_command> </test> </tests> <help> ====================== 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 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). .. class:: infomark This galaxy tool implements the first part of the Orthofinder program, e.g. the clustering of orthogroups of genes. If you have already ran OrthoFinder, the tool allows to re-run the analysis from the pre-computed blast-results. ----------- Input files ----------- - When using "from fasta" option (e.g Orthofinder from scratch) : the input files are a set of proteomes in fasta format (on file per species). Choose this option if you have no OrthoFinder results yet. - When using "from blast results" option : the input files are all the following files from of a previous OrthoFinder run (these files appear only if you have chosen to keep them while launching a previous run): - A dataset collection / multiple datasets for the blast outputs - A dataset collection / multiple datasets for .fa files - The SpeciesIDs.txt file - The SequencesIDs.txt file ---------- Parameters ---------- - Sequence search program : You can choose either blast, blast_gz, diamond, or diamond ultra-sensitive (diamond is faster) - Get the blast results : Check "Yes" if, while using blast as the sequence search program, you want to retrieve the blast output files - Inflation : the inflation parameter; modify this parameter is not recommended. </help> <expand macro="citations"/> </tool>