From 7707cfbe7cc2d7677460704cb4725bf36698f527 Mon Sep 17 00:00:00 2001
From: dorien-er <roosen.dorien@gmail.com>
Date: Tue, 6 Feb 2024 15:41:14 +0100
Subject: [PATCH] add script and config to list busco datasets

---
 src/busco/{ => busco}/config.vsh.yaml         |  0
 src/busco/{ => busco}/help.txt                |  0
 src/busco/{ => busco}/script.sh               |  0
 src/busco/{ => busco}/test.sh                 |  0
 src/busco/{ => busco}/test_data/genome.fna    |  0
 src/busco/{ => busco}/test_data/protein.fasta |  0
 src/busco/{ => busco}/test_data/script.sh     |  0
 src/busco/busco_list_datasets/config.vsh.yaml | 36 +++++++++++++++++++
 src/busco/busco_list_datasets/script.sh       |  6 ++++
 src/busco/busco_list_datasets/test.sh         |  6 ++++
 10 files changed, 48 insertions(+)
 rename src/busco/{ => busco}/config.vsh.yaml (100%)
 rename src/busco/{ => busco}/help.txt (100%)
 rename src/busco/{ => busco}/script.sh (100%)
 rename src/busco/{ => busco}/test.sh (100%)
 rename src/busco/{ => busco}/test_data/genome.fna (100%)
 rename src/busco/{ => busco}/test_data/protein.fasta (100%)
 rename src/busco/{ => busco}/test_data/script.sh (100%)
 create mode 100644 src/busco/busco_list_datasets/config.vsh.yaml
 create mode 100644 src/busco/busco_list_datasets/script.sh
 create mode 100644 src/busco/busco_list_datasets/test.sh

diff --git a/src/busco/config.vsh.yaml b/src/busco/busco/config.vsh.yaml
similarity index 100%
rename from src/busco/config.vsh.yaml
rename to src/busco/busco/config.vsh.yaml
diff --git a/src/busco/help.txt b/src/busco/busco/help.txt
similarity index 100%
rename from src/busco/help.txt
rename to src/busco/busco/help.txt
diff --git a/src/busco/script.sh b/src/busco/busco/script.sh
similarity index 100%
rename from src/busco/script.sh
rename to src/busco/busco/script.sh
diff --git a/src/busco/test.sh b/src/busco/busco/test.sh
similarity index 100%
rename from src/busco/test.sh
rename to src/busco/busco/test.sh
diff --git a/src/busco/test_data/genome.fna b/src/busco/busco/test_data/genome.fna
similarity index 100%
rename from src/busco/test_data/genome.fna
rename to src/busco/busco/test_data/genome.fna
diff --git a/src/busco/test_data/protein.fasta b/src/busco/busco/test_data/protein.fasta
similarity index 100%
rename from src/busco/test_data/protein.fasta
rename to src/busco/busco/test_data/protein.fasta
diff --git a/src/busco/test_data/script.sh b/src/busco/busco/test_data/script.sh
similarity index 100%
rename from src/busco/test_data/script.sh
rename to src/busco/busco/test_data/script.sh
diff --git a/src/busco/busco_list_datasets/config.vsh.yaml b/src/busco/busco_list_datasets/config.vsh.yaml
new file mode 100644
index 00000000..444e2a6d
--- /dev/null
+++ b/src/busco/busco_list_datasets/config.vsh.yaml
@@ -0,0 +1,36 @@
+functionality:
+  name: busco
+  description: Lists the available busco datasets
+  info:
+    keywords: [lineage datasets]
+    homepage: https://busco.ezlab.org/
+    documentation: https://busco.ezlab.org/busco_userguide.html
+    repository: https://gitlab.com/ezlab/busco
+    reference: "10.1007/978-1-4939-9173-0_14"
+    licence: MIT
+  argument_groups:
+    - name: Outputs
+      arguments:
+        - name: --output
+          alternatives: ["-o"]
+          direction: output
+          type: file
+          description: |
+            Output file of the available busco datasets
+          required: false
+          default: busco_dataset_list.txt
+          example: file.txt
+  resources:
+    - type: bash_script
+      path: script.sh
+  test_resources:
+    - type: bash_script
+      path: test.sh
+platforms:
+  - type: docker
+    image: quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0
+    setup:
+      - type: docker
+        run: |
+          busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt
+  - type: nextflow
diff --git a/src/busco/busco_list_datasets/script.sh b/src/busco/busco_list_datasets/script.sh
new file mode 100644
index 00000000..6c80725c
--- /dev/null
+++ b/src/busco/busco_list_datasets/script.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+busco --list-datasets | awk '/^#{40}/{flag=1; next} flag{print}' > $par_output
\ No newline at end of file
diff --git a/src/busco/busco_list_datasets/test.sh b/src/busco/busco_list_datasets/test.sh
new file mode 100644
index 00000000..053f41bc
--- /dev/null
+++ b/src/busco/busco_list_datasets/test.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+busco --list-datasets > $par_output 
\ No newline at end of file