Add agat sp filter feature from kill list

CHANGELOG.md

@@ -2,15 +2,17 @@
 
 ## NEW FUNCTIONALITY
 
-* `agat`:
-  - `agat/agat_convert_genscan2gff`: convert a genscan file into a GFF file (PR #100).
-
 * `bd_rhapsody/bd_rhapsody_sequence_analysis`: BD Rhapsody Sequence Analysis CWL pipeline (PR #96).
 
 * `rsem/rsem_calculate_expression`: Calculate expression levels (PR #93).
 
 * `nanoplot`: Plotting tool for long read sequencing data and alignments (PR #95).
 
+* `agat`:
+  - `agat/agat_convert_genscan2gff`: convert a genscan file into a GFF file (PR #100).
+  - `agat/agat_sp_filter_feature_from_kill_list`: remove features in a GFF file based on a kill list (PR #105).
+
+
 ## BREAKING CHANGES
 
 * `falco`: Fix a typo in the `--reverse_complement` argument (PR #157).
@@ -55,6 +57,7 @@
   - `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).
 
+
 * `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).
@@ -91,6 +94,7 @@
 
 * `trimgalore`: Quality and adapter trimming for fastq files (PR #117). 
 
+
 ## MINOR CHANGES
 
 * `busco` components: update BUSCO to `5.7.1` (PR #72).

src/agat/agat_sp_filter_feature_from_kill_list/config.vsh.yaml

@@ -0,0 +1,105 @@
+name: agat_sp_filter_feature_from_kill_list
+namespace: agat
+description: |
+  Remove features based on a kill list. The default behaviour is to look at the features's ID. 
+  If the feature has an ID (case insensitive) listed among the kill list it will be removed.
+  Removing a level1 or level2 feature will automatically remove all linked subfeatures, and 
+  removing all children of a feature will automatically remove this feature too.
+keywords: [gene annotations, filtering, gff]
+links:
+  homepage: https://github.com/NBISweden/AGAT
+  documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_filter_feature_from_kill_list.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 GFF3 file that will be read.
+        type: file
+        required: true
+      - name: --kill_list
+        alternatives: [--kl]
+        description: Text file containing the kill list. One value per line.
+        type: file
+        required: true
+        example: kill_list.txt
+  - name: Outputs
+    arguments:
+      - name: --output
+        alternatives: [-o, --out]
+        description: |
+          Path to the output GFF file that contains filtered features. 
+        type: file
+        direction: output
+        required: true
+  - name: Arguments
+    arguments:
+      - name: --type
+        alternatives: [-p, -l]
+        description: |
+          Primary tag option, case insensitive, list. Allow to specify the feature types that 
+          will be handled. 
+
+          You can specify a specific feature by giving its primary tag name (column 3) as: 
+
+            * cds
+            * Gene
+            * mRNA
+
+          You can specify directly all the feature of a particular
+          level: 
+
+            * level2=mRNA,ncRNA,tRNA,etc 
+            * level3=CDS,exon,UTR,etc. 
+
+          By default all features are taken into account. Fill the option with the value "all" will 
+          have the same behaviour.
+        type: string
+        multiple: true
+      - name: --attribute
+        alternatives: [-a]
+        description: |
+          Attribute tag to specify the attribute to analyse. Case sensitive. Default: ID
+        type: string
+        example: ID
+      - 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
+      - name: --verbose
+        alternatives: [-v]
+        description: Verbose option for debugging purpose.
+        type: boolean_true
+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_sp_filter_feature_from_kill_list/help.txt

@@ -0,0 +1,85 @@
+```sh
+agat_sp_filter_feature_from_kill_list.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_filter_feature_from_kill_list.pl
+
+Description:
+    The script aims to remove features based on a kill list. The default
+    behaviour is to look at the features's ID. If the feature has an ID
+    (case insensitive) listed among the kill list it will be removed. /!\
+    Removing a level1 or level2 feature will automatically remove all linked
+    subfeatures, and removing all children of a feature will automatically
+    remove this feature too.
+
+Usage:
+        agat_sp_filter_feature_from_kill_list.pl --gff infile.gff --kill_list file.txt  [ --output outfile ]
+        agat_sp_filter_feature_from_kill_list.pl --help
+
+Options:
+    -f, --reffile, --gff or -ref
+            Input GFF3 file that will be read
+
+    -p, --type or -l
+            primary tag option, case insensitive, list. Allow to specied the
+            feature types that will be handled. You can specified a specific
+            feature by given its primary tag name (column 3) as: cds, Gene,
+            MrNa You can specify directly all the feature of a particular
+            level: level2=mRNA,ncRNA,tRNA,etc level3=CDS,exon,UTR,etc By
+            default all feature are taking into account. fill the option by
+            the value "all" will have the same behaviour.
+
+    --kl or --kill_list
+            Kill list. One value per line.
+
+    -a or --attribute
+            Attribute tag to specify the attribute to analyse. Case
+            sensitive. Default: ID
+
+    -o or --output
+            Output GFF file. If no output file is specified, the output will
+            be written to STDOUT.
+
+    -v      Verbose option for debugging purpose.
+
+    -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_sp_filter_feature_from_kill_list/script.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+## VIASH END
+
+# unset flags
+[[ "$par_verbose" == "false" ]] && unset par_verbose
+
+# convert par_type to comma separated list
+par_type=$(echo $par_type | tr ';' ',')
+
+# run agat_sp_filter_feature_from_kill_list
+agat_sp_filter_feature_from_kill_list.pl \
+  --gff "$par_gff" \
+  --kill_list "$par_kill_list" \
+  --output "$par_output" \
+  ${par_type:+--type "${par_type}"} \
+  ${par_attribute:+--attribute "${par_attribute}"} \
+  ${par_config:+--config "${par_config}"} \
+  ${par_verbose:+-v}

src/agat/agat_sp_filter_feature_from_kill_list/test.sh

@@ -0,0 +1,36 @@
+#!/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" \
+  --gff "$test_dir/1_truncated.gff" \
+  --kill_list "$test_dir/kill_list.txt" \
+  --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/test_output.gff"
+if [ $? -ne 0 ]; then
+  echo "Output file output.gff does not match expected output"
+  exit 1
+fi
+
+echo "> Test successful"