| Previous changeset 7:7c55feb65057 (2022-01-24) Next changeset 9:e731ea24e48d (2022-02-09) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246" |
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modified:
metaspades.xml |
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added:
write_tsv_script.py |
| b |
| diff -r 7c55feb65057 -r f338e9942b27 metaspades.xml --- a/metaspades.xml Mon Jan 24 18:45:46 2022 +0000 +++ b/metaspades.xml Tue Jan 25 07:57:04 2022 +0000 |
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| @@ -136,12 +136,12 @@ <output_collection name="out_cr" type="list" count="3"> <element name="ecoli_1K.fastq.gz_1.00.0_0.cor"> <assert_contents> - <has_size value="130317" delta="1000"/> + <has_size value="130317" delta="5000"/> </assert_contents> </element> <element name="ecoli_1K.fastq.gz_2.00.0_0.cor"> <assert_contents> - <has_size value="130317" delta="1000"/> + <has_size value="130317" delta="5000"/> </assert_contents> </element> <element name="ecoli_1K.fastq.gz__unpaired.00.0_0.cor"> |
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| diff -r 7c55feb65057 -r f338e9942b27 write_tsv_script.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/write_tsv_script.py Tue Jan 25 07:57:04 2022 +0000 |
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| @@ -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)) |