Mercurial > repos > nml > spades
changeset 20:78ced22d09a2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
author | iuc |
---|---|
date | Wed, 13 Jul 2022 07:41:05 +0000 |
parents | 9be710099b99 |
children | a789e163a670 |
files | macros.xml spades.xml write_tsv_script.py |
diffstat | 3 files changed, 19 insertions(+), 3 deletions(-) [+] |
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--- a/macros.xml Mon May 09 22:49:43 2022 +0000 +++ b/macros.xml Wed Jul 13 07:41:05 2022 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">3.15.4</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
--- a/spades.xml Mon May 09 22:49:43 2022 +0000 +++ b/spades.xml Wed Jul 13 07:41:05 2022 +0000 @@ -161,8 +161,9 @@ </output> <output name="out_cs"> <assert_contents> - <has_n_lines n="1"/> + <has_n_lines n="2"/> <has_text_matching expression="#name	length	coverage"/> + <has_text_matching expression="NODE_1	1000	225.723888"/> </assert_contents> </output> <output name="out_l"> @@ -675,6 +676,21 @@ </assert_contents> </output> </test> + <!-- #17 Fix stats script --> + <test expect_num_outputs="1"> + <conditional name="singlePaired"> + <param name="sPaired" value="single"/> + <param name="input1" value="ecoli_1K.fastq.gz"/> + </conditional> + <param name="optional_output" value="ss"/> + <output name="out_ss"> + <assert_contents> + <has_n_lines n="2"/> + <has_text text="NODE_1	1000	140.620106"/> + <has_text_matching expression="#name	length	coverage"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ .. class:: infomark
--- a/write_tsv_script.py Mon May 09 22:49:43 2022 +0000 +++ b/write_tsv_script.py Wed Jul 13 07:41:05 2022 +0000 @@ -3,7 +3,7 @@ import re import sys -search_str = r"^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*).*\$" +search_str = r"^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*)(.*\$)?" replace_str = r"\1_\2\t\3\t\4"