| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/orthofinder_onlygroups/orthofinder_onlygroups/2.5.5+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/orthofinder_onlygroups/orthofinder_onlygroups/2.5.4+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/orthofinder_onlygroups/orthofinder_onlygroups/2.5.4+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/orthofinder_onlygroups/orthofinder_onlygroups/2.4.0+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/orthofinder_onlygroups/orthofinder_onlygroups/2.4.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/orthofinder_onlygroups/orthofinder_onlygroups/2.2.6 |
| toolshed.g2.bx.psu.edu/repos/iuc/orthofinder_onlygroups/orthofinder_onlygroups/2.1.2 |
| toolshed.g2.bx.psu.edu/repos/iuc/orthofinder_onlygroups/orthofinder_onlygroups/1.1.4 |
| orthofinder_onlygroups |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| orthofinder | 2.5.4 | package |
| util-linux | 2.36 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
init|input_fasta: ['inputs/no_fa_ext/AcAcaud_trinity', 'inputs/no_fa_ext/AmAmphi_trinity', 'inputs/no_fa_ext/ApApomp_trinity', 'inputs/no_fa_ext/AsAsp1_trinity'] init|search|search_program: diamond init|start: fasta trees|run_mode: -og inflation: 1.5 |
name: value name: value name: value name: 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 value |
| Test-2 |
init|input_fasta: ['inputs/proteomes/Mycoplasma_agalactiae.faa', 'inputs/proteomes/Mycoplasma_gallisepticum.faa', 'inputs/proteomes/Mycoplasma_genitalium.faa', 'inputs/proteomes/Mycoplasma_hyopneumoniae.faa'] init|search|search_program: diamond init|start: fasta trees|run_mode: -og inflation: 1.5 |
name: value name: value name: value name: value |
inputs/proteomes/Mycoplasma_agalactiae.faa inputs/proteomes/Mycoplasma_gallisepticum.faa inputs/proteomes/Mycoplasma_genitalium.faa inputs/proteomes/Mycoplasma_hyopneumoniae.faa value |
| Test-3 |
init|input_fasta: ['inputs/proteomes/Mycoplasma_agalactiae.faa', 'inputs/proteomes/Mycoplasma_gallisepticum.faa', 'inputs/proteomes/Mycoplasma_genitalium.faa', 'inputs/proteomes/Mycoplasma_hyopneumoniae.faa'] init|search|keepblastout: True init|search|search_program: blast init|start: fasta trees|run_mode: -og inflation: 1.5 |
name: value name: value name: value name: value name: value |
inputs/proteomes/Mycoplasma_agalactiae.faa inputs/proteomes/Mycoplasma_gallisepticum.faa inputs/proteomes/Mycoplasma_genitalium.faa inputs/proteomes/Mycoplasma_hyopneumoniae.faa value |
| Test-4 |
init|input_fasta: ['inputs/proteomes/Mycoplasma_agalactiae.faa', 'inputs/proteomes/Mycoplasma_gallisepticum.faa', 'inputs/proteomes/Mycoplasma_genitalium.faa', 'inputs/proteomes/Mycoplasma_hyopneumoniae.faa'] init|search|keepblastout: False init|search|search_program: blast init|start: fasta trees|run_mode: -og inflation: 1.5 |
name: value name: value name: value name: value |
inputs/proteomes/Mycoplasma_agalactiae.faa inputs/proteomes/Mycoplasma_gallisepticum.faa inputs/proteomes/Mycoplasma_genitalium.faa inputs/proteomes/Mycoplasma_hyopneumoniae.faa value |
| Test-5 |
init|input_blast_out: list collection init|input_blast_fa: list collection init|specIDs: inputs/blastids/SpeciesIDs.txt init|seqIDs: inputs/blastids/SequenceIDs.txt init|start: blast trees|run_mode: -og inflation: 1.5 |
name: value name: value name: value name: value name: value name: value |
inputs/blastout/Blast0_0.txt inputs/blastout/Blast0_1.txt inputs/blastout/Blast0_2.txt inputs/blastout/Blast0_3.txt inputs/blastout/Blast1_0.txt inputs/blastout/Blast1_1.txt inputs/blastout/Blast1_2.txt inputs/blastout/Blast1_3.txt inputs/blastout/Blast2_0.txt inputs/blastout/Blast2_1.txt inputs/blastout/Blast2_2.txt inputs/blastout/Blast2_3.txt inputs/blastout/Blast3_0.txt inputs/blastout/Blast3_1.txt inputs/blastout/Blast3_2.txt inputs/blastout/Blast3_3.txt inputs/blastfa/Species0.fa inputs/blastfa/Species1.fa inputs/blastfa/Species2.fa inputs/blastfa/Species3.fa inputs/blastids/SpeciesIDs.txt inputs/blastids/SequenceIDs.txt value |
| Test-6 |
init|input_fasta: ['inputs/proteomes/Mycoplasma_agalactiae.faa', 'inputs/proteomes/Mycoplasma_gallisepticum.faa', 'inputs/proteomes/Mycoplasma_genitalium.faa', 'inputs/proteomes/Mycoplasma_hyopneumoniae.faa'] init|search|search_program: diamond init|start: fasta trees|run_mode: full inflation: 1.5 |
name: value name: value name: value name: value name: value |
inputs/proteomes/Mycoplasma_agalactiae.faa inputs/proteomes/Mycoplasma_gallisepticum.faa inputs/proteomes/Mycoplasma_genitalium.faa inputs/proteomes/Mycoplasma_hyopneumoniae.faa value |
| Test-7 |
init|input_fasta: ['inputs/proteomes/Mycoplasma_agalactiae.faa', 'inputs/proteomes/Mycoplasma_gallisepticum.faa', 'inputs/proteomes/Mycoplasma_genitalium.faa', 'inputs/proteomes/Mycoplasma_hyopneumoniae.faa'] init|search|search_program: diamond init|start: fasta trees|run_mode: full inflation: 1.5 output_duplications: True |
name: value name: value name: value name: value name: value name: value name: value name: value name: value |
inputs/proteomes/Mycoplasma_agalactiae.faa inputs/proteomes/Mycoplasma_gallisepticum.faa inputs/proteomes/Mycoplasma_genitalium.faa inputs/proteomes/Mycoplasma_hyopneumoniae.faa value |
| Test-8 |
init|input_fasta: ['inputs/no_fa_ext/AcAcaud_trinity', 'inputs/no_fa_ext/AmAmphi_trinity', 'inputs/no_fa_ext/ApApomp_trinity', 'inputs/no_fa_ext/AsAsp1_trinity'] init|search|search_program: diamond init|start: fasta trees|run_mode: -og inflation: 1.5 |
name: value name: value name: value name: 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 value |
| Test-9 |
init|input_fasta: ['inputs/proteomes/Mycoplasma_agalactiae.faa', 'inputs/proteomes/Mycoplasma_gallisepticum.faa', 'inputs/proteomes/Mycoplasma_genitalium.faa', 'inputs/proteomes/Mycoplasma_hyopneumoniae.faa'] init|search|search_program: diamond init|start: fasta trees|tree_method|msa_program: muscle trees|tree_method|msa_tree_program: raxml trees|tree_method|method: msa trees|run_mode: full inflation: 1.5 |
name: value name: value name: value name: value |
inputs/proteomes/Mycoplasma_agalactiae.faa inputs/proteomes/Mycoplasma_gallisepticum.faa inputs/proteomes/Mycoplasma_genitalium.faa inputs/proteomes/Mycoplasma_hyopneumoniae.faa value |