/tools/emboss_5/emboss_maskfeat.xml
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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>