add script and config to list busco datasets

viash-hub · Feb 6, 2024 · 7707cfb · 7707cfb
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diff --git a/src/busco/config.vsh.yaml → src/busco/busco/config.vsh.yaml b/src/busco/config.vsh.yaml → src/busco/busco/config.vsh.yaml
diff --git a/src/busco/help.txt → src/busco/busco/help.txt b/src/busco/help.txt → src/busco/busco/help.txt
diff --git a/src/busco/script.sh → src/busco/busco/script.sh b/src/busco/script.sh → src/busco/busco/script.sh
diff --git a/src/busco/test.sh → src/busco/busco/test.sh b/src/busco/test.sh → src/busco/busco/test.sh
diff --git a/src/busco/test_data/genome.fna → src/busco/busco/test_data/genome.fna b/src/busco/test_data/genome.fna → src/busco/busco/test_data/genome.fna
diff --git a/src/busco/test_data/protein.fasta → src/busco/busco/test_data/protein.fasta b/src/busco/test_data/protein.fasta → src/busco/busco/test_data/protein.fasta
diff --git a/src/busco/test_data/script.sh → src/busco/busco/test_data/script.sh b/src/busco/test_data/script.sh → 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
@@ -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
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+busco --list-datasets | awk '/^#{40}/{flag=1; next} flag{print}' > $par_output
diff --git a/src/busco/busco_list_datasets/test.sh b/src/busco/busco_list_datasets/test.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+busco --list-datasets > $par_output