Merge branch 'main' into add-agat_sp_complement_annotations

CHANGELOG.md

@@ -20,16 +20,18 @@
                 based on a provided sequence IDs or region coordinates file (PR #85).
 
 * `agat`:
-  - `agat_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).
-  - `/agat_convert_bed2gff`: convert bed file to gff format (PR #97).
+  - `agat/agat_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).
+  - `agat/agat_convert_bed2gff`: convert bed file to gff format (PR #97).
+  - `agat/agat_convert_embl2gff`: convert an EMBL file into GFF format (PR #99).
+  - `agat/agat_convert_sp_gff2tsv`: convert gtf/gff file into tabulated file (PR #102).
+  - `agat/agat_convert_sp_gxf2gxf`: fixes and/or standardizes any GTF/GFF file into full sorted GTF/GFF file (PR #103).
   - `agat_sp_complement_annotations`: complement a reference annotation with other annotations (PR #129).
 
 * `bedtools`:
   - `bedtools/bedtools_intersect`: Allows one to screen for overlaps between two sets of genomic features (PR #94).
   - `bedtools/bedtools_sort`: Sorts a feature file (bed/gff/vcf) by chromosome and other criteria (PR #98).
-
-
-* `agat/agat_convert_embl2gff`: convert an EMBL file into GFF format (PR #99).
+  - `bedtools/bedtools_bamtofastq`: Convert BAM alignments to FASTQ files (PR #101).
+  - `bedtools/bedtools_bedtobam`: Converts genomic feature records (bed/gff/vcf) to BAM format (PR #111).
 
 ## MINOR CHANGES
 

src/agat/agat_convert_sp_gff2tsv/config.vsh.yaml

@@ -0,0 +1,70 @@
+name: agat_convert_sp_gff2tsv
+namespace: agat
+description: |
+    The script aims to convert gtf/gff file into tabulated file. Attribute's
+    tags from the 9th column become column titles.
+keywords: [gene annotations, GFF conversion]
+links:
+  homepage: https://github.com/NBISweden/AGAT
+  documentation: https://agat.readthedocs.io/en/latest/tools/agat_convert_sp_gff2tsv.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
+authors:
+  - __merge__: /src/_authors/leila_paquay.yaml
+    roles: [ author, maintainer ]
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --gff
+        alternatives: [-f]
+        description: Input GTF/GFF file.
+        type: file
+        required: true
+        direction: input
+        example: input.gff
+  - name: Outputs
+    arguments:       
+      - name: --output
+        alternatives: [-o, --out, --outfile]
+        description: Output GFF file. If no output file is specified, the output will be written to STDOUT.
+        type: file
+        direction: output
+        required: true
+        example: output.gff
+  - name: Arguments
+    arguments:
+      - name: --config
+        alternatives: [-c]
+        description: |
+          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).        
+        type: file
+        required: false
+        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

src/agat/agat_convert_sp_gff2tsv/help.txt

@@ -0,0 +1,63 @@
+```sh
+agat_convert_sp_gff2tsv.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_convert_sp_gff2tsv.pl
+
+Description:
+    The script aims to convert gtf/gff file into tabulated file. Attribute's
+    tags from the 9th column become column titles.
+
+Usage:
+        agat_convert_sp_gff2tsv.pl -gff file.gff [ -o outfile ]
+        agat_convert_sp_gff2tsv.pl --help
+
+Options:
+    --gff or -f
+            Input GTF/GFF file.
+
+    -o , --output , --out or --outfile
+            Output GFF file. If no output file is specified, the output will
+            be written to STDOUT.
+
+    -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).
+
+    -h or --help
+            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

src/agat/agat_convert_sp_gff2tsv/script.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+agat_convert_sp_gff2tsv.pl \
+  -f "$par_gff" \
+  -o "$par_output" \
+  ${par_config:+--config "${par_config}"}

src/agat/agat_convert_sp_gff2tsv/test.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+test_dir="${meta_resources_dir}/test_data"
+out_dir="${meta_resources_dir}/out_data"
+
+echo "> Run $meta_name with test data"
+"$meta_executable" \
+  --gff "$test_dir/1.gff" \
+  --output "$out_dir/output.gff" 
+
+echo ">> Checking output"
+[ ! -f "$out_dir/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "$out_dir/output.gff" ] && echo "Output file output.gff is empty" && exit 1
+
+echo ">> Check if output matches expected output"
+diff "$out_dir/output.gff" "$test_dir/agat_convert_sp_gff2tsv_1.tsv"
+if [ $? -ne 0 ]; then
+  echo "Output file output.gff does not match expected output"
+  exit 1
+fi
+
+echo "> Test successful"