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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,64 @@ | ||
| name: agat_sp_add_introns | ||
| namespace: agat | ||
| description: | | ||
| Add intronic elements to a gtf/gff file without intron features. | ||
| keywords: [gene annotations, GTF conversion] | ||
| links: | ||
| homepage: https://github.com/NBISweden/AGAT | ||
| documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_add_introns.html | ||
| issue_tracker: https://github.com/NBISweden/AGAT/issues | ||
| repository: https://github.com/NBISweden/AGAT | ||
| references: | ||
| doi: 10.5281/zenodo.3552717 | ||
| 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: [-f, --ref, --reffile] | ||
| description: Input GTF/GFF file. | ||
| type: file | ||
| required: true | ||
| example: input.gff | ||
| - name: Outputs | ||
| arguments: | ||
| - name: --output | ||
| alternatives: [-o, --out, --outfile, --gtf] | ||
| description: Output GFF3 file. | ||
| type: file | ||
| direction: output | ||
| required: true | ||
| example: output.gff | ||
| - name: Arguments | ||
| arguments: | ||
| - 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 | ||
| example: custom_agat_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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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| ```sh | ||
| agat_sp_add_introns.pl --help | ||
| ``` | ||
|
|
||
| ------------------------------------------------------------------------------ | ||
| | Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0 | | ||
| | https://github.com/NBISweden/AGAT | | ||
| | National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se | | ||
| ------------------------------------------------------------------------------ | ||
|
|
||
|
|
||
| Name: | ||
| agat_sp_add_introns.pl | ||
|
|
||
| Description: | ||
| The script aims to add intron features to gtf/gff file without intron | ||
| features. | ||
|
|
||
| Usage: | ||
| agat_sp_add_introns.pl --gff infile --out outFile | ||
| agat_sp_add_introns.pl --help | ||
|
|
||
| Options: | ||
| --gff, -f, --ref or -reffile | ||
| Input GTF/GFF file. | ||
|
|
||
| --out, --output or -o | ||
| Output GFF3 file. | ||
|
|
||
| -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). | ||
|
|
||
| --help or -h | ||
| Display this helpful text. | ||
|
|
||
| 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: | ||
|
|
||
| https://github.com/NBISweden/AGAT/issues | ||
|
|
||
| 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. | ||
|
|
||
| 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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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,11 @@ | ||
| #!/bin/bash | ||
|
|
||
| set -eo pipefail | ||
|
|
||
| ## VIASH START | ||
| ## VIASH END | ||
|
|
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| agat_sp_add_introns.pl \ | ||
| -f "$par_gff" \ | ||
| -o "$par_output" \ | ||
| ${par_config:+--config "${par_config}"} |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,34 @@ | ||
| #!/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 | ||
|
|
||
| echo "> Run $meta_name with test data" | ||
| "$meta_executable" \ | ||
| --gff "$test_dir/1_truncated.gff" \ | ||
| --output "$TMPDIR/output.gff" | ||
|
|
||
| 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/test_output.gff" | ||
| if [ $? -ne 0 ]; then | ||
| echo "Output file output.gff does not match expected output" | ||
| exit 1 | ||
| fi | ||
| echo "> Test successful" |
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