Mercurial > repos > iuc > vsearch
diff masking.xml @ 0:fae6527990af draft
Imported from capsule None
author | iuc |
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date | Thu, 21 May 2015 03:58:09 -0400 |
parents | |
children | f29e21388219 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/masking.xml Thu May 21 03:58:09 2015 -0400 @@ -0,0 +1,79 @@ +<tool id="vsearch_masking" name="VSearch masking" version="@VERSION@.0"> + <description></description> + <macros> + <import>vsearch_macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> +<![CDATA[ + vsearch + @GENERAL@ + #if $qmask != 'no': + --qmask $qmask + #end if + $hardmask + --maskfasta "$infile" + --output $outfile + +]]> + </command> + <inputs> + <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--maskfasta)" /> + <expand macro="qmask" /> + <expand macro="hardmask" /> + </inputs> + <outputs> + <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="infile" value="db.fasta" ftype="fasta" /> + <param name="qmask" value="dust"/> + <param name="hardmask" value="True"/> + <output name="outfile" file="masking_result1.fasta" ftype="fasta" /> + </test> + <test> + <param name="infile" value="db.fasta" ftype="fasta" /> + <param name="qmask" value="soft"/> + <param name="hardmask" value="True"/> + <output name="outfile" file="masking_result2.fasta" ftype="fasta" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +An input sequence can be composed of lower- or uppercase nucleotides. Lowercase nucleotides +are silently set to uppercase before masking, unless the −−qmask soft option is used. +Here are the results of combined masking options −−qmask (or −−dbmask for database sequences) and −−hardmask, assuming each input sequences contains both lower and uppercase nucleotides: + +===== ======== ================================================ +qmask hardmask action +===== ======== ================================================ +none off no masking, all symbols uppercased +none on no masking, all symbols uppercased +dust off masked symbols lowercased, others uppercased +dust on masked symbols changed to Ns, others uppercased +soft off lowercase symbols masked, no case changes +soft on lowercase symbols masked and changed to Ns +===== ======== ================================================ + +Masking options + --hardmask mask by replacing with N instead of lower case + --maskfasta FILENAME mask sequences in the given FASTA file + --output FILENAME output to specified FASTA file + --qmask mask seqs with "dust", "soft" or "none" method (dust) + +@EXTERNAL_DOCUMENTATION@ + +------- + +@REFERENCES@ + + +]]> + </help> + <expand macro="citations" /> +</tool>