Previous changeset 15:a39c4cb6ab7f (2022-01-24) Next changeset 17:7897763d14ec (2022-02-09) |
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246" |
modified:
spades.xml |
added:
write_tsv_script.py |
b |
diff -r a39c4cb6ab7f -r d2d1df21dfb9 spades.xml --- a/spades.xml Mon Jan 24 18:43:37 2022 +0000 +++ b/spades.xml Tue Jan 25 07:55:17 2022 +0000 |
b |
@@ -308,12 +308,12 @@ <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"> @@ -340,12 +340,12 @@ <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"> @@ -404,12 +404,12 @@ <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"> @@ -436,12 +436,12 @@ <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"> |
b |
diff -r a39c4cb6ab7f -r d2d1df21dfb9 write_tsv_script.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/write_tsv_script.py Tue Jan 25 07:55:17 2022 +0000 |
b |
@@ -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)) |