feat: Bustools text (#509)

* [fix] (template): Missing code in wrappers' doc. Error #187

* Wrapper tested

* test written

* format

* file extension set to tsv

* Update bio/bustools/text/environment.yaml

Co-authored-by: tdayris <tdayris@gustaveroussy.fr>
Co-authored-by: tdayris <thibault.dayris@gustaveroussy.fr>
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>

bio/bustools/text/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - bustools =0.41

bio/bustools/text/meta.yaml

@@ -0,0 +1,13 @@
+name: bustools text
+description: convert bus to tsv files
+url: https://github.com/BUStools/bustools#text
+author:
+  - Thibault Dayris
+input:
+  - list of bus files
+output:
+  - Path to TSV output
+params:
+  - extra: Optional parameters, besides `--o/-output`
+notes: |
+  When multiple bus files are provided, only one TSV file is produced.

bio/bustools/text/test/Snakefile

@@ -0,0 +1,26 @@
+rule test_bustools_text:
+    input:
+        "file.bus",
+    output:
+        "file.tsv",
+    threads: 1
+    params:
+        extra="",
+    log:
+        "logs/bustools.log",
+    wrapper:
+        "master/bio/bustools/text"
+
+
+rule test_bustools_text_list:
+    input:
+        ["file.bus", "file2.bus"],
+    output:
+        "file2.tsv",
+    threads: 1
+    params:
+        extra="--flags --pad",
+    log:
+        "logs/bustools.log",
+    wrapper:
+        "master/bio/bustools/text"

bio/bustools/text/wrapper.py

@@ -0,0 +1,21 @@
+#!/usr/bin/env python3
+# conding: utf-8
+
+"""snakemake wrapper for bustool text"""
+
+
+__author__ = "Thibault Dayris"
+__copyright__ = "Copyright 2022, Thibault Dayris"
+__email__ = "thibault.dayris@gustaveroussy.fr"
+__license__ = "MIT"
+
+from snakemake.shell import shell
+
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+extra = snakemake.params.get("extra", "")
+
+bus_files = snakemake.input[0]
+if isinstance(bus_files, list):
+    bus_files = " ".join(bus_files)
+
+shell("bustools text --output {snakemake.output[0]} {extra} {bus_files} {log}")

test.py

@@ -239,6 +239,18 @@ def test_biobambam2_bamsormadup():
     )
 
 
+@skip_if_not_modified
+def test_bustools_text():
+    run(
+        "bio/bustools/text",
+        ["snakemake", "--cores", "1", "file.tsv", "--use-conda", "-F"]
+    )
+    run(
+        "bio/bustools/text",
+        ["snakemake", "--cores", "1", "file2.tsv", "--use-conda", "-F"]
+    )
+
+
 @skip_if_not_modified
 def test_open_cravat_run():
     run(