/tools/emboss_5/emboss_maskfeat.xml

 1<tool id="EMBOSS: maskfeat50" name="maskfeat" version="5.0.0">
 2  <description>Mask off features of a sequence</description>
 3  <command>maskfeat -sequence $input1 -outseq $out_file1 -type "$type" -tolower $tolower -maskchar "$maskchar" -osformat2 $out_format1 -auto</command>
 4  <inputs>
 5    <param format="data" name="input1" type="data">
 6      <label>Sequence</label>
 7    </param>
 8    <param name="type" size="50" type="text" value="repeat*">
 9      <label>Feature to mask</label>
10    </param>
11    <param name="tolower" type="select">
12      <label>Mask features by converting to lowercase</label>
13      <option value="no">No</option>
14      <option value="yes">Yes</option>
15    </param>
16    <param name="maskchar" size="1" type="text" value="N">
17      <label>Character to mask with</label>
18    </param>
19    <param name="out_format1" type="select">
20      <label>Output Sequence File Format</label>
21      <option value="fasta">FASTA (m)</option>
22      <option value="acedb">ACeDB (m)</option>
23      <option value="asn1">ASN.1 (m)</option>
24      <option value="clustal">Clustal (m)</option>
25      <option value="codata">CODATA (m)</option>
26      <option value="embl">EMBL (m)</option>
27      <option value="fitch">Fitch (m)</option>
28      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
29      <option value="genbank">GENBANK (m)</option>
30      <option value="gff">GFF (m)</option>
31      <option value="hennig86">Hennig86 (m)</option>
32      <option value="ig">Intelligenetics (m)</option>
33      <option value="jackknifer">Jackknifer (m)</option>
34      <option value="jackknifernon">Jackknifernon (m)</option>
35      <option value="mega">Mega (m)</option>
36      <option value="meganon">Meganon (m)</option>
37      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
38      <option value="pir">NBRF (PIR) (m)</option>
39      <option value="ncbi">NCBI style FASTA (m)</option>
40      <option value="nexus">Nexus/PAUP (m)</option>
41      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
42      <option value="phylip">PHYLIP interleaved (m)</option>
43      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
44      <option value="selex">SELEX (m)</option>
45      <option value="staden">Staden (s)</option>
46      <option value="strider">DNA strider (m)</option>
47      <option value="swiss">SwisProt entry (m)</option>
48      <option value="text">Plain sequence (s)</option>
49      <option value="treecon">Treecon (m)</option>
50    </param>
51  </inputs>
52  <outputs>
53    <data format="fasta" name="out_file1" />
54  </outputs>
55  <tests>
56    <test>
57      <param name="input1" value="2.fasta"/>
58      <param name="type" value="repeat*"/>
59      <param name="tolower" value="no"/>
60      <param name="maskchar" value="N"/>
61      <param name="out_format1" value="fasta"/>
62      <output name="out_file1" file="emboss_maskfeat_out.fasta"/>
63    </test>
64  </tests>
65  <code file="emboss_format_corrector.py" />
66  <help>
67    You can view the original documentation here_.
68    
69    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/maskfeat.html
70  </help>
71</tool>