Mercurial > repos > iuc > spades_rnaviralspades
changeset 2:249f6a28c751 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
| author | iuc |
|---|---|
| date | Tue, 25 Jan 2022 07:55:39 +0000 |
| parents | 11d7955eddf9 |
| children | d159735a6a9f |
| files | rnaviralspades.xml write_tsv_script.py |
| diffstat | 2 files changed, 18 insertions(+), 2 deletions(-) [+] |
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--- a/rnaviralspades.xml Mon Jan 24 18:44:03 2022 +0000 +++ b/rnaviralspades.xml Tue Jan 25 07:55:39 2022 +0000 @@ -149,12 +149,12 @@ <output_collection name="out_cr" type="list" count="2"> <element name="ecoli_1K_1.fastq.gz.fastq0_0.cor"> <assert_contents> - <has_size value="34468" delta="1000"/> + <has_size value="34468" delta="2000"/> </assert_contents> </element> <element name="ecoli_1K_2.fastq.gz.fastq0_0.cor"> <assert_contents> - <has_size value="34468" delta="1000"/> + <has_size value="34468" delta="2000"/> </assert_contents> </element> </output_collection>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/write_tsv_script.py Tue Jan 25 07:55:39 2022 +0000 @@ -0,0 +1,16 @@ +#!/usr/bin/env python + +import re +import sys + +search_str = r"^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*).*\$" + +replace_str = r"\1_\2\t\3\t\4" + +cmd = re.compile(search_str) + +sys.stdout.write("#name\tlength\tcoverage\n") + +for i, line in enumerate(sys.stdin): + if cmd.match(line): + sys.stdout.write(cmd.sub(replace_str, line))