view rapsodyn/fastaGroomerForMakeBlastdb.xml @ 7:3f7b0788a1c4 draft

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<tool id="fastaGroomerForMakeBlastdb" name="fastaGroomerForMakeBlastdb" version="1.00">
<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>