Add agat sp ensembl output style #130
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| name: agat_sp_ensembl_output_style | ||||||
| namespace: agat | ||||||
| description: | | ||||||
| This script takes a normal gff3 annotation format file and convert it to | ||||||
| gff3 like ensembl format. | ||||||
|
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| keywords: [gene annotations, GFF conversion] | ||||||
| links: | ||||||
| homepage: https://github.com/NBISweden/AGAT | ||||||
| documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_ensembl_output_style.html | ||||||
| issue_tracker: https://github.com/NBISweden/AGAT/issues | ||||||
| repository: https://github.com/NBISweden/AGAT | ||||||
| references: | ||||||
| doi: 10.5281/zenodo.3552717 | ||||||
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| license: GPL-3.0 | ||||||
| requirements: | ||||||
| - commands: [agat] | ||||||
| authors: | ||||||
| - __merge__: /src/_authors/leila_paquay.yaml | ||||||
| roles: [ author, maintainer ] | ||||||
| argument_groups: | ||||||
| - name: Inputs | ||||||
| arguments: | ||||||
| - name: --gff | ||||||
| alternatives: [-g, --ref] | ||||||
| description: Input GTF/GFF file. | ||||||
| type: file | ||||||
| required: true | ||||||
| direction: input | ||||||
| example: input.gff | ||||||
| - name: Outputs | ||||||
| arguments: | ||||||
| - name: --output | ||||||
| alternatives: [-o] | ||||||
| description: Output GFF file. | ||||||
| type: file | ||||||
| direction: output | ||||||
| required: true | ||||||
| example: output.gff | ||||||
| - name: Arguments | ||||||
| arguments: | ||||||
| - name: --verbose | ||||||
| alternatives: [-v] | ||||||
| description: Verbose option to see the warning messages when parsing the GFF file. | ||||||
| type: boolean_true | ||||||
| - name: --config | ||||||
| alternatives: [-c] | ||||||
| description: | | ||||||
| AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. The `--config` option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). | ||||||
| type: file | ||||||
| required: false | ||||||
| example: custom_config.yaml | ||||||
| resources: | ||||||
| - type: bash_script | ||||||
| path: script.sh | ||||||
| test_resources: | ||||||
| - type: bash_script | ||||||
| path: test.sh | ||||||
| - type: file | ||||||
| path: test_data | ||||||
| engines: | ||||||
| - type: docker | ||||||
| image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0 | ||||||
| setup: | ||||||
| - type: docker | ||||||
| run: | | ||||||
| agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt | ||||||
| runners: | ||||||
| - type: executable | ||||||
| - type: nextflow | ||||||
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| ```sh | ||
| agat_sp_ensembl_output_style.pl --help | ||
| ``` | ||
|
|
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| ------------------------------------------------------------------------------ | ||
| | Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0 | | ||
| | https://github.com/NBISweden/AGAT | | ||
| | National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se | | ||
| ------------------------------------------------------------------------------ | ||
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| Name: | ||
| agat_sp_ensembl_output_style.pl | ||
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| Description: | ||
| This script takes a normal gff3 annotation format file and convert it to | ||
| gff3 like ensembl format. | ||
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| Usage: | ||
| agat_sp_ensembl_output_style.pl -g infile.gff [ -o outfile ] | ||
| agat_sp_ensembl_output_style.pl --help | ||
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| Options: | ||
| -g, --gff or -ref | ||
| Input GTF/GFF file. | ||
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| -v Verbose option to see the warning messages when parsing the gff | ||
| file. | ||
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| -o or --output | ||
| Output GFF file. If no output file is specified, the output will | ||
| be written to STDOUT. | ||
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| -c or --config | ||
| String - Input agat config file. By default AGAT takes as input | ||
| agat_config.yaml file from the working directory if any, | ||
| otherwise it takes the orignal agat_config.yaml shipped with | ||
| AGAT. To get the agat_config.yaml locally type: "agat config | ||
| --expose". The --config option gives you the possibility to use | ||
| your own AGAT config file (located elsewhere or named | ||
| differently). | ||
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| -h or --help | ||
| Display this helpful text. | ||
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| Feedback: | ||
| Did you find a bug?: | ||
| Do not hesitate to report bugs to help us keep track of the bugs and | ||
| their resolution. Please use the GitHub issue tracking system available | ||
| at this address: | ||
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| https://github.com/NBISweden/AGAT/issues | ||
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| Ensure that the bug was not already reported by searching under Issues. | ||
| If you're unable to find an (open) issue addressing the problem, open a new one. | ||
| Try as much as possible to include in the issue when relevant: | ||
| - a clear description, | ||
| - as much relevant information as possible, | ||
| - the command used, | ||
| - a data sample, | ||
| - an explanation of the expected behaviour that is not occurring. | ||
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| Do you want to contribute?: | ||
| You are very welcome, visit this address for the Contributing | ||
| guidelines: | ||
| https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md |
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| #!/bin/bash | ||
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| set -eo pipefail | ||
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| ## VIASH START | ||
| ## VIASH END | ||
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| # unset flags | ||
| [[ "$par_verbose" == "false" ]] && unset par_verbose | ||
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| # run agat_sp_ensembl_output_style.pl | ||
| agat_sp_ensembl_output_style.pl \ | ||
| --gff "$par_gff" \ | ||
| --output "$par_output" \ | ||
| ${par_verbose:+-v} | ||
| ${par_config:+--config "${par_config}"} \ |
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| #!/bin/bash | ||
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| set -eo pipefail | ||
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| ## VIASH START | ||
| ## VIASH END | ||
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| test_dir="${meta_resources_dir}/test_data" | ||
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| # create temporary directory and clean up on exit | ||
| TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX") | ||
| function clean_up { | ||
| [[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR" | ||
| } | ||
| trap clean_up EXIT | ||
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| echo "> Run $meta_name with test data" | ||
| "$meta_executable" \ | ||
| --gff "$test_dir/0.gff" \ | ||
| --output "$TMPDIR/output.gff" | ||
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| echo ">> Checking output" | ||
| [ ! -f "$TMPDIR/output.gff" ] && echo "Output file output.gff does not exist" && exit 1 | ||
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| echo ">> Check if output is empty" | ||
| [ ! -s "$TMPDIR/output.gff" ] && echo "Output file output.gff is empty" && exit 1 | ||
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| echo ">> Check if output matches expected output" | ||
| diff "$TMPDIR/output.gff" "$test_dir/agat_sp_ensembl_output_style_1.gff" | ||
| if [ $? -ne 0 ]; then | ||
| echo "Output file output.gff does not match expected output" | ||
| exit 1 | ||
| fi | ||
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| echo "> Test successful" |
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| Original file line number | Diff line number | Diff line change |
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| ##gff-version 3 | ||
| scaffold625 maker gene 337818 343277 . + . ID=CLUHARG00000005458;Name=TUBB3_2 | ||
| scaffold625 maker mRNA 337818 343277 . + . ID=CLUHART00000008717;Parent=CLUHARG00000005458 | ||
| scaffold625 maker exon 337818 337971 . + . ID=CLUHART00000008717:exon:1404;Parent=CLUHART00000008717 | ||
| scaffold625 maker exon 340733 340841 . + . ID=CLUHART00000008717:exon:1405;Parent=CLUHART00000008717 | ||
| scaffold625 maker exon 341518 341628 . + . ID=CLUHART00000008717:exon:1406;Parent=CLUHART00000008717 | ||
| scaffold625 maker exon 341964 343277 . + . ID=CLUHART00000008717:exon:1407;Parent=CLUHART00000008717 | ||
| scaffold625 maker CDS 337915 337971 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717 | ||
| scaffold625 maker CDS 340733 340841 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717 | ||
| scaffold625 maker CDS 341518 341628 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717 | ||
| scaffold625 maker CDS 341964 343033 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717 | ||
| scaffold625 maker five_prime_UTR 337818 337914 . + . ID=CLUHART00000008717:five_prime_utr;Parent=CLUHART00000008717 | ||
| scaffold625 maker three_prime_UTR 343034 343277 . + . ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717 | ||
| scaffold789 maker gene 558184 564780 . + . ID=CLUHARG00000003852;Name=PF11_0240 | ||
| scaffold789 maker mRNA 558184 564780 . + . ID=CLUHART00000006146;Parent=CLUHARG00000003852 | ||
| scaffold789 maker exon 558184 560123 . + . ID=CLUHART00000006146:exon:995;Parent=CLUHART00000006146 | ||
| scaffold789 maker exon 561401 561519 . + . ID=CLUHART00000006146:exon:996;Parent=CLUHART00000006146 | ||
| scaffold789 maker exon 564171 564235 . + . ID=CLUHART00000006146:exon:997;Parent=CLUHART00000006146 | ||
| scaffold789 maker exon 564372 564780 . + . ID=CLUHART00000006146:exon:998;Parent=CLUHART00000006146 | ||
| scaffold789 maker CDS 558191 560123 . + 0 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146 | ||
| scaffold789 maker CDS 561401 561519 . + 2 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146 | ||
| scaffold789 maker CDS 564171 564235 . + 0 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146 | ||
| scaffold789 maker CDS 564372 564588 . + 1 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146 | ||
| scaffold789 maker five_prime_UTR 558184 558190 . + . ID=CLUHART00000006146:five_prime_utr;Parent=CLUHART00000006146 | ||
| scaffold789 maker three_prime_UTR 564589 564780 . + . ID=CLUHART00000006146:three_prime_utr;Parent=CLUHART00000006146 | ||
| scaffold789 maker mRNA 558184 564780 . + . ID=CLUHART00000006147;Parent=CLUHARG00000003852 | ||
| scaffold789 maker exon 558184 560123 . + . ID=CLUHART00000006147:exon:997;Parent=CLUHART00000006147 | ||
| scaffold789 maker exon 561401 561519 . + . ID=CLUHART00000006147:exon:998;Parent=CLUHART00000006147 | ||
| scaffold789 maker exon 562057 562121 . + . ID=CLUHART00000006147:exon:999;Parent=CLUHART00000006147 | ||
| scaffold789 maker exon 564372 564780 . + . ID=CLUHART00000006147:exon:1000;Parent=CLUHART00000006147 | ||
| scaffold789 maker CDS 558191 560123 . + 0 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147 | ||
| scaffold789 maker CDS 561401 561519 . + 2 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147 | ||
| scaffold789 maker CDS 562057 562121 . + 0 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147 | ||
| scaffold789 maker CDS 564372 564588 . + 1 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147 | ||
| scaffold789 maker five_prime_UTR 558184 558190 . + . ID=CLUHART00000006147:five_prime_utr;Parent=CLUHART00000006147 | ||
| scaffold789 maker three_prime_UTR 564589 564780 . + . ID=CLUHART00000006147:three_prime_utr;Parent=CLUHART00000006147 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| ##gff-version 3 | ||
| scaffold625 maker gene 337818 343277 . + . ID=CLUHARG00000005458;Name=TUBB3_2;gene_id=CLUHARG00000005458 | ||
| scaffold625 maker transcript 337818 343277 . + . ID=CLUHART00000008717;Parent=CLUHARG00000005458;transcript_id=CLUHART00000008717 | ||
| scaffold625 maker exon 337818 337971 . + . ID=CLUHART00000008717:exon:1404;Parent=CLUHART00000008717;exon_id=CLUHART00000008717:exon:1404 | ||
| scaffold625 maker exon 340733 340841 . + . ID=CLUHART00000008717:exon:1405;Parent=CLUHART00000008717;exon_id=CLUHART00000008717:exon:1405 | ||
| scaffold625 maker exon 341518 341628 . + . ID=CLUHART00000008717:exon:1406;Parent=CLUHART00000008717;exon_id=CLUHART00000008717:exon:1406 | ||
| scaffold625 maker exon 341964 343277 . + . ID=CLUHART00000008717:exon:1407;Parent=CLUHART00000008717;exon_id=CLUHART00000008717:exon:1407 | ||
| scaffold625 maker CDS 337915 337971 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717 | ||
| scaffold625 maker CDS 340733 340841 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717 | ||
| scaffold625 maker CDS 341518 341628 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717 | ||
| scaffold625 maker CDS 341964 343033 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717 | ||
| scaffold625 maker five_prime_UTR 337818 337914 . + . ID=CLUHART00000008717:five_prime_utr;Parent=CLUHART00000008717 | ||
| scaffold625 maker three_prime_UTR 343034 343277 . + . ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717 | ||
| scaffold789 maker gene 558184 564780 . + . ID=CLUHARG00000003852;Name=PF11_0240;gene_id=CLUHARG00000003852 | ||
| scaffold789 maker transcript 558184 564780 . + . ID=CLUHART00000006146;Parent=CLUHARG00000003852;transcript_id=CLUHART00000006146 | ||
| scaffold789 maker exon 558184 560123 . + . ID=CLUHART00000006146:exon:995;Parent=CLUHART00000006146;exon_id=CLUHART00000006146:exon:995 | ||
| scaffold789 maker exon 561401 561519 . + . ID=CLUHART00000006146:exon:996;Parent=CLUHART00000006146;exon_id=CLUHART00000006146:exon:996 | ||
| scaffold789 maker exon 564171 564235 . + . ID=CLUHART00000006146:exon:997;Parent=CLUHART00000006146;exon_id=CLUHART00000006146:exon:997 | ||
| scaffold789 maker exon 564372 564780 . + . ID=CLUHART00000006146:exon:998;Parent=CLUHART00000006146;exon_id=CLUHART00000006146:exon:998 | ||
| scaffold789 maker CDS 558191 560123 . + 0 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146 | ||
| scaffold789 maker CDS 561401 561519 . + 2 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146 | ||
| scaffold789 maker CDS 564171 564235 . + 0 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146 | ||
| scaffold789 maker CDS 564372 564588 . + 1 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146 | ||
| scaffold789 maker five_prime_UTR 558184 558190 . + . ID=CLUHART00000006146:five_prime_utr;Parent=CLUHART00000006146 | ||
| scaffold789 maker three_prime_UTR 564589 564780 . + . ID=CLUHART00000006146:three_prime_utr;Parent=CLUHART00000006146 | ||
| scaffold789 maker transcript 558184 564780 . + . ID=CLUHART00000006147;Parent=CLUHARG00000003852;transcript_id=CLUHART00000006147 | ||
| scaffold789 maker exon 558184 560123 . + . ID=CLUHART00000006147:exon:997;Parent=CLUHART00000006147;exon_id=CLUHART00000006147:exon:997 | ||
| scaffold789 maker exon 561401 561519 . + . ID=CLUHART00000006147:exon:998;Parent=CLUHART00000006147;exon_id=CLUHART00000006147:exon:998 | ||
| scaffold789 maker exon 562057 562121 . + . ID=CLUHART00000006147:exon:999;Parent=CLUHART00000006147;exon_id=CLUHART00000006147:exon:999 | ||
| scaffold789 maker exon 564372 564780 . + . ID=CLUHART00000006147:exon:1000;Parent=CLUHART00000006147;exon_id=CLUHART00000006147:exon:1000 | ||
| scaffold789 maker CDS 558191 560123 . + 0 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147 | ||
| scaffold789 maker CDS 561401 561519 . + 2 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147 | ||
| scaffold789 maker CDS 562057 562121 . + 0 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147 | ||
| scaffold789 maker CDS 564372 564588 . + 1 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147 | ||
| scaffold789 maker five_prime_UTR 558184 558190 . + . ID=CLUHART00000006147:five_prime_utr;Parent=CLUHART00000006147 | ||
| scaffold789 maker three_prime_UTR 564589 564780 . + . ID=CLUHART00000006147:three_prime_utr;Parent=CLUHART00000006147 |
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| @@ -0,0 +1,10 @@ | ||
| #!/bin/bash | ||
|
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| # clone repo | ||
| if [ ! -d /tmp/agat_source ]; then | ||
| git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source | ||
| fi | ||
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| # copy test data | ||
| cp -r /tmp/agat_source/t/scripts_output/in/0.gff src/agat/agat_sp_ensembl_output_style/test_data/ | ||
| cp -r /tmp/agat_source/t/scripts_output/out/agat_sp_ensembl_output_style_1.gff src/agat/agat_sp_ensembl_output_style/test_data/ |
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