Mercurial > repos > richard-burhans > batched_lastz
changeset 6:34d51e66256c draft
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz commit 2ab3532f7a45153eb0f945ac22c37cdcaea8c1e1
| author | richard-burhans |
|---|---|
| date | Wed, 10 Jul 2024 18:00:34 +0000 |
| parents | a68e128cdb1a |
| children | 4cd7884635c2 |
| files | batched_lastz.xml run_lastz_tarball.py test-data/input.tgz test-data/output.maf.gz |
| diffstat | 4 files changed, 12 insertions(+), 5 deletions(-) [+] |
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--- a/batched_lastz.xml Wed May 01 19:09:34 2024 +0000 +++ b/batched_lastz.xml Wed Jul 10 18:00:34 2024 +0000 @@ -17,10 +17,16 @@ <param argument="--input" type="data" format="tgz" label="Tarball"/> </inputs> <outputs> - <data name="output" label="Output"/> + <data name="output" label="Output" format="maf"/> </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input" value="input.tgz" ftype="tgz"/> + <output name="output" decompress="true" file="output.maf.gz" ftype="maf"/> + </test> + </tests> <help><![CDATA[ - TODO: Fill in help. + Run batched lastz ]]></help> <expand macro="citations"/> </tool>
--- a/run_lastz_tarball.py Wed May 01 19:09:34 2024 +0000 +++ b/run_lastz_tarball.py Wed Jul 10 18:00:34 2024 +0000 @@ -8,12 +8,12 @@ import queue import re import shutil +import subprocess import sys -import subprocess import tarfile import tempfile +import time import typing -import time lastz_output_format_regex = re.compile( @@ -69,7 +69,7 @@ if stderr is not None: try: statinfo = os.stat(stderr, follow_symlinks=False) - except: + except Exception: statinfo = None if statinfo is None: @@ -305,6 +305,7 @@ for file_type, file_list in self.output_files.items(): with open(f"output.{file_type}", "w") as ofh: + print("##maf version=1", file=ofh) for filename in file_list: with open(f"galaxy/files/{filename}") as ifh: for line in ifh: