Add agat convert minimap2 bam2gff

CHANGELOG.md

@@ -79,6 +79,7 @@
   - `agat_convert_embl2gff`: convert an EMBL file into GFF format (PR #99).
   - `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_minimap2_bam2gff`: convert output from minimap2 (bam or sam) into gff file (PR #113).
   - `agat/agat_convert_mfannot2gff`: convert MFannot "masterfile" annotation to gff format (PR #112).
   - `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).

src/agat/agat_convert_minimap2_bam2gff/config.vsh.yaml

@@ -0,0 +1,75 @@
+name: agat_convert_minimap2_bam2gff
+namespace: agat
+description: |
+  Convert output from minimap2 (bam or sam) into gff file. To
+  get bam from minimap2 use the following command: `minimap2 -ax splice:hq
+  genome.fa Asecodes_parviclava.nucest.fa | samtools sort -O BAM -o
+  output.bam`. 
+keywords: [gene annotations, GFF conversion, minimap2]
+links:
+  homepage: https://github.com/NBISweden/AGAT
+  documentation: https://agat.readthedocs.io/en/latest/tools/agat_convert_minimap2_bam2gff.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: --input
+        alternatives: [-i]
+        description: Input file in SAM (.sam extension) or BAM (.bam extension) format.
+        type: file
+        required: true
+        direction: input
+        example: input.sam
+  - name: Outputs
+    arguments:
+      - name: --output
+        alternatives: [-o, --out]
+        description: Output GFF file.
+        type: file
+        direction: output
+        required: true
+        example: output.gff
+  - name: Arguments
+    arguments:
+      - name: --bam
+        alternatives: [-b]
+        description: To force the use of the input file as a BAM file.
+        type: boolean_true
+      - name: --sam
+        alternatives: [-s]
+        description: To force the use of the input file as a SAM 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_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_minimap2_bam2gff/help.txt

@@ -0,0 +1,76 @@
+```sh
+agat_convert_minimap2_bam2gff.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_minimap2_bam2gff.pl
+
+Description:
+    The script converts output from minimap2 (bam or sam) into gff file. To
+    get bam from minimap2 use the following command: minimap2 -ax splice:hq
+    genome.fa Asecodes_parviclava.nucest.fa | samtools sort -O BAM -o
+    output.bam To use bam with this script you will need samtools in your
+    path.
+
+Usage:
+        agat_convert_minimap2_bam2gff.pl -i infile.bam [ -o outfile ]
+        agat_convert_minimap2_bam2gff.pl -i infile.sam [ -o outfile ]
+        agat_convert_minimap2_bam2gff.pl --help
+
+Options:
+    if ( !GetOptions( 'i|input=s' => \$opt_in,
+
+    -i or --input
+            Input file in sam (.sam extension) or bam (.bam extension)
+            format.
+
+    -b or --bam
+            To force to use the input file as sam file.
+
+    -s or --sam
+            To force to use the input file as sam file.
+
+    -o, --out or --output
+            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_minimap2_bam2gff/script.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+## VIASH END
+
+# unset flags
+[[ "$par_bam" == "false" ]] && unset par_bam
+[[ "$par_sam" == "false" ]] && unset par_sam
+
+# run agat_convert_sp_bed2gff.pl
+agat_convert_minimap2_bam2gff.pl \
+  --input "$par_input" \
+  --output "$par_output" \
+  ${par_bam:+--bam} \
+  ${par_sam:+--sam} \
+  ${par_config:+--config "${par_config}"}

src/agat/agat_convert_minimap2_bam2gff/test.sh

@@ -0,0 +1,35 @@
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+## VIASH END
+
+test_dir="${meta_resources_dir}/test_data"
+
+# create temporary directory and clean up on exit
+TMPDIR=$(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" \
+  --input "$test_dir/test_minimap2.sam" \
+  --output "$TMPDIR/output.gff" 
+
+echo ">> Checking output"
+[ ! -f "$TMPDIR/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "$TMPDIR/output.gff" ] && echo "Output file output.gff is empty" && exit 1
+
+echo ">> Check if output matches expected output"
+diff "$TMPDIR/output.gff" "$test_dir/agat_convert_minimap2_bam2gff_1.gff"
+if [ $? -ne 0 ]; then
+  echo "Output file output.gff does not match expected output"
+  exit 1
+fi
+
+echo "> Test successful"