Mercurial > repos > mcharles > rapsosnp
diff rapsodyn/fastaGroomerForMakeBlastdb.xml @ 0:442a7c88b886 draft
Uploaded
author | mcharles |
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date | Wed, 10 Sep 2014 09:18:15 -0400 |
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children | 3f7b0788a1c4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/fastaGroomerForMakeBlastdb.xml Wed Sep 10 09:18:15 2014 -0400 @@ -0,0 +1,20 @@ +<tool id="fastaGroomerForMakeBlastdb" name="fastaGroomerForMakeBlastdb" version="0.01"> +<description>fasta Groomer For MakeBlastdb</description> +<command interpreter="perl"> + fastaGroomerForMakeBlastdb.pl $input_fasta > $output_fasta +</command> +<inputs> + <param name="input_fasta" type="data" format="fasta" label="Select a suitable input FASTA file from your history"/> +</inputs> +<outputs> + <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string}"/> +</outputs> + +<help> +MakeBlastDb has several warning handled has error which is problematic on galaxyn This groomer ensure that the fasta file will not generate this warnings / error : + +- First line of the sequence is more than 40% of N => replace all the 'N' of the first line by 'a' (not elegant but low impact and efficient) + +- Header line should not have [xxx=xxx] kind of text because MakeBlastdb try to interpret it => remove the [] when this feature is detected +</help> +</tool>