| Previous changeset 2:c9e10e0d6c10 (2015-08-24) |
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Commit message:
fix inputs clean name |
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modified:
STACKS_procrad.xml stacks.py |
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| diff -r c9e10e0d6c10 -r 0e0ff9e9c761 STACKS_procrad.xml --- a/STACKS_procrad.xml Mon Aug 24 15:39:12 2015 +0000 +++ b/STACKS_procrad.xml Mon Sep 28 13:21:35 2015 +0000 |
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| @@ -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 "> |
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| diff -r c9e10e0d6c10 -r 0e0ff9e9c761 stacks.py --- a/stacks.py Mon Aug 24 15:39:12 2015 +0000 +++ b/stacks.py Mon Sep 28 13:21:35 2015 +0000 |
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| @@ -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 |