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1 <tool id="fastaGroomerForMakeBlastdb" name="fastaGroomerForMakeBlastdb" version="0.01">
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2 <description>fasta Groomer For MakeBlastdb</description>
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3 <command interpreter="perl">
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4 fastaGroomerForMakeBlastdb.pl $input_fasta > $output_fasta
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5 </command>
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6 <inputs>
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7 <param name="input_fasta" type="data" format="fasta" label="Select a suitable input FASTA file from your history"/>
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8 </inputs>
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9 <outputs>
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10 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string}"/>
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11 </outputs>
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12
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13 <help>
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14 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 :
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15
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16 - 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)
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17
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18 - Header line should not have [xxx=xxx] kind of text because MakeBlastdb try to interpret it => remove the [] when this feature is detected
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19 </help>
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20 </tool>
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