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comparison masking.xml @ 0:fae6527990af draft

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Imported from capsule None
author iuc
date Thu, 21 May 2015 03:58:09 -0400
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children f29e21388219
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-1:000000000000 0:fae6527990af
1 <tool id="vsearch_masking" name="VSearch masking" version="@VERSION@.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@
13 #if $qmask != 'no':
14 --qmask $qmask
15 #end if
16 $hardmask
17 --maskfasta "$infile"
18 --output $outfile
19
20 ]]>
21 </command>
22 <inputs>
23 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--maskfasta)" />
24 <expand macro="qmask" />
25 <expand macro="hardmask" />
26 </inputs>
27 <outputs>
28 <data name="outfile" format="fasta" label="${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 @REFERENCES@
74
75
76 ]]>
77 </help>
78 <expand macro="citations" />
79 </tool>