Mercurial > repos > mcharles > rapsosnp
comparison rapsodyn/fastaGroomerForMakeBlastdb.xml @ 0:442a7c88b886 draft
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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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-1:000000000000 | 0:442a7c88b886 |
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1 <tool id="fastaGroomerForMakeBlastdb" name="fastaGroomerForMakeBlastdb" version="0.01"> | |
2 <description>fasta Groomer For MakeBlastdb</description> | |
3 <command interpreter="perl"> | |
4 fastaGroomerForMakeBlastdb.pl $input_fasta > $output_fasta | |
5 </command> | |
6 <inputs> | |
7 <param name="input_fasta" type="data" format="fasta" label="Select a suitable input FASTA file from your history"/> | |
8 </inputs> | |
9 <outputs> | |
10 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string}"/> | |
11 </outputs> | |
12 | |
13 <help> | |
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 : | |
15 | |
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) | |
17 | |
18 - Header line should not have [xxx=xxx] kind of text because MakeBlastdb try to interpret it => remove the [] when this feature is detected | |
19 </help> | |
20 </tool> |