Mercurial > repos > rnateam > splitfasta
changeset 0:bc25ba9d9fcf draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hacked/splitFasta commit fcd6ef7e59971abd6b6a3a5401f92bcdef6ef76c
| author | rnateam |
|---|---|
| date | Sun, 05 Jul 2015 08:37:52 -0400 |
| parents | |
| children | 279e2625de3a |
| files | splitFasta.py splitfasta.xml |
| diffstat | 2 files changed, 37 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/splitFasta.py Sun Jul 05 08:37:52 2015 -0400 @@ -0,0 +1,14 @@ +import sys, os +if __name__ == "__main__": + #assuming perfect input, read every two lines + inpath = sys.argv[1] + file_contents = open(inpath, 'r').readlines() + os.makedirs('splits') + inname = os.path.basename(inpath) + for i in range(0, len(file_contents), 2): + headline = file_contents[i] + outname = headline[1:headline.index(' ')]+'.fa' + outfile = open(os.path.join('splits',outname), 'w') + outfile.write(file_contents[i]) + outfile.write(file_contents[i+1]) + outfile.close()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/splitfasta.xml Sun Jul 05 08:37:52 2015 -0400 @@ -0,0 +1,23 @@ +<tool id="rbc_splitfasta" name="SplitFasta" version="0.1.0"> + <requirements> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + + <command interpreter="python"> + <![CDATA[ + splitFasta.py $inputFile; echo 'blah' > blah + ]]></command> + <inputs> + <param name="inputFile" type="data" format="txt" label="Fasta file to split"/> + </inputs> + <outputs> + <collection type="list"> + <discover_datasets pattern="(?P<designation>.*)" directory="splits" visible="false"/> + </collection> + </outputs> + <help><![CDATA[ + Takes an input file and writes each consecutive two lines to a separate file, in a dataset collection. + ]]></help> +</tool>