Mercurial > repos > cmonjeau > stacks
changeset 3:0e0ff9e9c761 default tip
fix inputs clean name
| author | cmonjeau |
|---|---|
| date | Mon, 28 Sep 2015 13:21:35 +0000 |
| parents | c9e10e0d6c10 |
| children | |
| files | STACKS_procrad.xml stacks.py |
| diffstat | 2 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/STACKS_procrad.xml Mon Aug 24 15:39:12 2015 +0000 +++ b/STACKS_procrad.xml Mon Sep 28 13:21:35 2015 +0000 @@ -236,7 +236,7 @@ <outputs> <data format="txt" name="output" label="results.log with ${tool.name} on ${on_string}: demultiplexed and cleaned reads" /> - <data format="txt" name="additional" label="fast(a/q) file with ${tool.name}" hidden="true"> + <data format="txt" name="additional" label="fasta/fastq file with ${tool.name}" hidden="true"> <discover_datasets pattern="__designation_and_ext__" directory="galaxy_outputs" visible="true" /> </data> <data format="zip" name="output_archive" label="all_files.zip with ${tool.name} on ${on_string}: demultiplexed and cleaned reads ">
--- a/stacks.py Mon Aug 24 15:39:12 2015 +0000 +++ b/stacks.py Mon Sep 28 13:21:35 2015 +0000 @@ -35,7 +35,7 @@ for line in open(input_config, "r").readlines(): if line.strip() != '': extract=line.strip().split("::") - tab_files[extract[0].replace(" (", ".").replace(" ", ".").replace(")", "").replace(":", ".").replace("/", ".")]=extract[1] + tab_files[extract[0].replace("(", ".").replace(" ", ".").replace(")", "").replace(":", ".").replace("/", ".")]=extract[1] # tabfiles[name]-> path return tab_files @@ -47,12 +47,12 @@ for line in open(input_config, "r").readlines(): if line.strip() != '': extract=line.strip().split("::") - parse_name=re.search("^STACKS.*\((.*\.[ATCG]*\.fq)\)$", extract[0]) + parse_name=re.search("STACKS.*\((.*\.[ATCG]*).*\)$", extract[0]) # rename galaxy name in a short name if parse_name: extract[0]=parse_name.groups(1)[0] - tab_files[extract[0].replace(" (", ".").replace(" ", ".").replace(")", "").replace(":", ".").replace("/", ".")]=extract[1] + tab_files[extract[0].replace("(", ".").replace(" ", ".").replace(")", "").replace(":", ".").replace("/", ".")]=extract[1] # tabfiles[name]-> path return tab_files