Mercurial > repos > iuc > vsearch
annotate masking.xml @ 2:f29e21388219 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
| author | iuc |
|---|---|
| date | Thu, 17 Dec 2015 12:53:39 -0500 |
| parents | fae6527990af |
| children | 4258854759ba |
| rev | line source |
|---|---|
|
2
f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
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changeset
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1 <tool id="vsearch_masking" name="VSearch masking" version="@VERSION@.1"> |
| 0 | 2 <description></description> |
| 3 <macros> | |
| 4 <import>vsearch_macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <expand macro="version_command" /> | |
| 9 <command> | |
| 10 <![CDATA[ | |
| 11 vsearch | |
| 12 @GENERAL@ | |
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2
f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
|
13 #if str( $qmask ) != 'no': |
|
f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
|
14 --qmask "$qmask" |
| 0 | 15 #end if |
| 16 $hardmask | |
| 17 --maskfasta "$infile" | |
|
2
f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
|
18 --output "$outfile" |
| 0 | 19 |
| 20 ]]> | |
| 21 </command> | |
| 22 <inputs> | |
| 23 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--maskfasta)" /> | |
| 24 <expand macro="qmask" /> | |
| 25 <expand macro="hardmask" /> | |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" /> | |
| 29 </outputs> | |
| 30 <tests> | |
| 31 <test> | |
| 32 <param name="infile" value="db.fasta" ftype="fasta" /> | |
| 33 <param name="qmask" value="dust"/> | |
| 34 <param name="hardmask" value="True"/> | |
| 35 <output name="outfile" file="masking_result1.fasta" ftype="fasta" /> | |
| 36 </test> | |
| 37 <test> | |
| 38 <param name="infile" value="db.fasta" ftype="fasta" /> | |
| 39 <param name="qmask" value="soft"/> | |
| 40 <param name="hardmask" value="True"/> | |
| 41 <output name="outfile" file="masking_result2.fasta" ftype="fasta" /> | |
| 42 </test> | |
| 43 </tests> | |
| 44 <help> | |
| 45 <![CDATA[ | |
| 46 **What it does** | |
| 47 | |
| 48 An input sequence can be composed of lower- or uppercase nucleotides. Lowercase nucleotides | |
| 49 are silently set to uppercase before masking, unless the −−qmask soft option is used. | |
| 50 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: | |
| 51 | |
| 52 ===== ======== ================================================ | |
| 53 qmask hardmask action | |
| 54 ===== ======== ================================================ | |
| 55 none off no masking, all symbols uppercased | |
| 56 none on no masking, all symbols uppercased | |
| 57 dust off masked symbols lowercased, others uppercased | |
| 58 dust on masked symbols changed to Ns, others uppercased | |
| 59 soft off lowercase symbols masked, no case changes | |
| 60 soft on lowercase symbols masked and changed to Ns | |
| 61 ===== ======== ================================================ | |
| 62 | |
| 63 Masking options | |
| 64 --hardmask mask by replacing with N instead of lower case | |
| 65 --maskfasta FILENAME mask sequences in the given FASTA file | |
| 66 --output FILENAME output to specified FASTA file | |
| 67 --qmask mask seqs with "dust", "soft" or "none" method (dust) | |
| 68 | |
| 69 @EXTERNAL_DOCUMENTATION@ | |
| 70 | |
| 71 | |
| 72 ]]> | |
| 73 </help> | |
| 74 <expand macro="citations" /> | |
| 75 </tool> |