[ { "id": "trimal", "name": "trimAl", "article": "10.1093\/bioinformatics\/btp348", "website": "http:\/\/trimal.cgenomics.org\/", "git": "https:\/\/github.com\/scapella\/trimal", "description": "trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment", "version": "1.4.1", "documentation": "http:\/\/trimal.cgenomics.org\/getting_started_with_trimal_v1.2", "multiqc": "custom", "commands": [ { "name": "trimal", "cname": "trimAl", "command": "trimal", "category": "phylogenetics", "output_dir": "trimal", "inputs": [ { "name": "sequences_in", "type": [ "aligned_fasta", "phylip" ], "file": "", "description": "Aligned sequences file", "from": "parameter" } ], "outputs": [ { "name": "clean_seqs", "type": [ "aligned_fasta", "phylip" ], "file": "out.*", "description": "Cleaned aligned sequences file" }, { "name": "report", "type": "html", "file": "trimAl_report_mqc.html", "description": "Report file" } ], "options": [ { "name": "trimal_sequences_in", "type": "input_file", "value": "", "label": "Path to aligned sequences file" }, { "name": "trimal_out_format", "type": "radio", "choices": [ { "Same as input": "" }, { "fasta": "-fasta" }, { "phylip": "-phylip" } ], "value": "", "label": "Output file format" }, { "name": "trimal_ignorestopcodon", "prefix": "-ignorestopcodon", "type": "checkbox", "value": false, "label": "Ignore stop codons in the input coding sequences" }, { "name": "trimal_splitbystopcodon", "prefix": "-splitbystopcodon", "type": "checkbox", "value": false, "label": "Split input coding sequences up to first stop codon appearance" }, { "name": "trimal_colnumbering", "prefix": "-colnumbering", "type": "checkbox", "value": false, "label": "Get the relationship between the columns in the old and new alignment." }, { "name": "trimal_gapthreshold", "prefix": "-gt", "type": "numeric", "value": 1, "min": 0, "max": 1, "step": "NA", "label": "gapthreshold: 1 - (fraction of sequences with a gap allowed)" }, { "name": "trimal_simthreshold", "prefix": "-st", "type": "numeric", "value": 1, "min": 0, "max": 1, "step": "NA", "label": "Minimum average similarity allowed" }, { "name": "trimal_cons", "prefix": "-cons", "type": "numeric", "value": 100, "min": 0, "max": 100, "step": 1, "label": "Minimum percentage of the positions in the original alignment to conserve" }, { "name": "trimal_nogaps", "prefix": "-nogaps", "type": "checkbox", "value": false, "label": "Remove all positions with gaps in the alignment" }, { "name": "trimal_noallgaps", "prefix": "-noallgaps", "type": "checkbox", "value": false, "label": "Remove columns composed only by gaps" }, { "name": "trimal_keepseqs", "prefix": "-keepseqs", "type": "checkbox", "value": false, "label": "Keep sequences even if they are composed only by gaps" }, { "name": "trimal_block", "prefix": "-block", "type": "numeric", "value": 0, "min": "NA", "max": "NA", "step": "NA", "label": "Minimum column block size to be kept in the trimmed alignment. Available with manual and automatic (gappyout) methods" }, { "name": "trimal_resoverlap", "prefix": "-resoverlap", "type": "numeric", "value": 0, "min": 0, "max": 1, "step": "NA", "label": "Minimum overlap of a positions with other positions in the column to be considered a good position" }, { "name": "trimal_seqoverlap", "prefix": "-seqoverlap", "type": "numeric", "value": 0, "min": 0, "max": 100, "step": 1, "label": "Minimum percentage of good positions that a sequence must have in order to be conserved" } ] } ], "install": [], "citations": { "trimal": [ "Salvador Capella-Guti\u00e9rrez, Jos\u00e9 M. Silla-Mart\u00ednez, Toni Gabald\u00f3n, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, Volume 25, Issue 15, 1 August 2009, Pages 1972-1973, https:\/\/doi.org\/10.1093\/bioinformatics\/btp348" ] }, "yaml": "{\n id: trimal,\n name: trimAl ,\n article: \"10.1093\/bioinformatics\/btp348\",\n website: \"http:\/\/trimal.cgenomics.org\/\",\n git: \"https:\/\/github.com\/scapella\/trimal\",\n description: \"trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment\",\n version: \"1.4.1\",\n documentation: \"http:\/\/trimal.cgenomics.org\/getting_started_with_trimal_v1.2\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: trimal,\n cname: \"trimAl\",\n command: \"trimal\",\n category: \"phylogenetics\",\n output_dir: trimal,\n inputs: [{ name: sequences_in, type: [\"aligned_fasta\",\"phylip\"], file: \"\", description: \"Aligned sequences file\", from: \"parameter\"}],\n outputs: [{ name: clean_seqs, type: [\"aligned_fasta\",\"phylip\"], file: \"out.*\", description: \"Cleaned aligned sequences file\"},\n { name: report, type: \"html\", file: \"trimAl_report_mqc.html\", description: \"Report file\"}\n ],\n options: [\n {\n name: trimal_sequences_in,\n type: input_file,\n value: \"\",\n label: \"Path to aligned sequences file\",\n },\n {\n name: trimal_out_format,\n type: radio,\n choices:\n [\n Same as input: \"\",\n fasta: \"-fasta\",\n phylip: \"-phylip\"\n ],\n value: \"\",\n label: \"Output file format\",\n },\n {\n name: trimal_ignorestopcodon,\n prefix: \"-ignorestopcodon\",\n type: checkbox,\n value: False,\n label: \"Ignore stop codons in the input coding sequences\",\n },\n {\n name: trimal_splitbystopcodon,\n prefix: \"-splitbystopcodon\",\n type: checkbox,\n value: False,\n label: \"Split input coding sequences up to first stop codon appearance\",\n },\n {\n name: trimal_colnumbering,\n prefix: \"-colnumbering\",\n type: checkbox,\n value: False,\n label: \"Get the relationship between the columns in the old and new alignment.\",\n },\n {\n name: \"trimal_gapthreshold\",\n prefix: \"-gt\",\n type: \"numeric\",\n value: 1,\n min: 0,\n max: 1,\n step: NA,\n label: \"gapthreshold: 1 - (fraction of sequences with a gap allowed)\",\n },\n {\n name: \"trimal_simthreshold\",\n prefix: \"-st\",\n type: \"numeric\",\n value: 1,\n min: 0,\n max: 1,\n step: NA,\n label: \"Minimum average similarity allowed\",\n },\n {\n name: \"trimal_cons\",\n prefix: \"-cons\",\n type: \"numeric\",\n value: 100,\n min: 0,\n max: 100,\n step: 1,\n label: \"Minimum percentage of the positions in the original alignment to conserve\",\n },\n {\n name: trimal_nogaps,\n prefix: \"-nogaps\",\n type: checkbox,\n value: False,\n label: \"Remove all positions with gaps in the alignment\",\n },\n {\n name: trimal_noallgaps,\n prefix: \"-noallgaps\",\n type: checkbox,\n value: False,\n label: \"Remove columns composed only by gaps\",\n },\n {\n name: trimal_keepseqs,\n prefix: \"-keepseqs\",\n type: checkbox,\n value: False,\n label: \"Keep sequences even if they are composed only by gaps\",\n },\n {\n name: \"trimal_block\",\n prefix: \"-block\",\n type: \"numeric\",\n value: 0,\n min: NA,\n max: NA,\n step: NA,\n label: \"Minimum column block size to be kept in the trimmed alignment. Available with manual and automatic (gappyout) methods\",\n },\n {\n name: \"trimal_resoverlap\",\n prefix: \"-resoverlap\",\n type: \"numeric\",\n value: 0,\n min: 0,\n max: 1,\n step: NA,\n label: \"Minimum overlap of a positions with other positions in the column to be considered a good position\",\n },\n {\n name: \"trimal_seqoverlap\",\n prefix: \"-seqoverlap\",\n type: \"numeric\",\n value: 0,\n min: 0,\n max: 100,\n step: 1,\n label: \"Minimum percentage of good positions that a sequence must have in order to be conserved\",\n },\n ],\n },\n ],\n install:\n {\n # trimal: [\n # \"cd \/opt\/biotools\/\",\n # \"wget -O trimal_v1.4.1.tar.gz https:\/\/github.com\/scapella\/trimal\/archive\/v1.4.1.tar.gz\",\n # \"tar -xvzf trimal_v1.4.1.tar.gz\",\n # \"cd trimal-1.4.1\/source\",\n # \"make -j 8\",\n # \"mv statal trimal readal -t \/opt\/biotools\/bin\",\n # \"cd \/opt\/biotools\",\n # \"rm -r trimal-1.4.1 trimal_v1.4.1.tar.gz\"\n # ]\n },\n citations:\n {\n trimal: [\n \"Salvador Capella-Guti\u00e9rrez, Jos\u00e9 M. Silla-Mart\u00ednez, Toni Gabald\u00f3n, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, Volume 25, Issue 15, 1 August 2009, Pages 1972-1973, https:\/\/doi.org\/10.1093\/bioinformatics\/btp348\"\n ]\n },\n}\n" } ]