Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_extractfeat.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="EMBOSS: extractfeat34" name="extractfeat" version="5.0.0"> | |
| 2 <!-- tool tested with documentation, functional test not designed due to empty files resulting from test input sequences --> | |
| 3 <description>Extract features from a sequence</description> | |
| 4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 5 <command>extractfeat -sequence $input1 -outseq $out_file1 -before $before -after $after -source "$source" -type "$type" -sense $sense -minscore $minscore -maxscore $maxscore -tag "$tag" -value | |
| 6 "$value" -join $join -featinname $featinname -describe "$describe" -osformat2 $out_format1 -auto</command> | |
| 7 <inputs> | |
| 8 <param format="data" name="input1" type="data"> | |
| 9 <label>Sequences</label> | |
| 10 </param> | |
| 11 <param name="before" size="4" type="text" value="0"> | |
| 12 <label>Number of bases or residues before the feature to include in the extracted sequence</label> | |
| 13 </param> | |
| 14 <param name="after" size="4" type="text" value="0"> | |
| 15 <label>Number of bases or residues after the feature to include in the extracted sequence</label> | |
| 16 </param> | |
| 17 <param name="source" size="4" type="text" value="*"> | |
| 18 <label>Feature source</label> | |
| 19 </param> | |
| 20 <param name="type" size="4" type="text" value="*"> | |
| 21 <label>Feature type</label> | |
| 22 </param> | |
| 23 <param name="sense" type="select"> | |
| 24 <label>Feature sense</label> | |
| 25 <option value="0">Any sense</option> | |
| 26 <option value="1">Forward sense</option> | |
| 27 <option value="-1">Reverse sense</option> | |
| 28 </param> | |
| 29 <param name="minscore" size="4" type="text" value="0.0"> | |
| 30 <label>Minimum score</label> | |
| 31 </param> | |
| 32 <param name="maxscore" size="4" type="text" value="0.0"> | |
| 33 <label>Maximum score</label> | |
| 34 </param> | |
| 35 <param name="tag" size="4" type="text" value="*"> | |
| 36 <label>Feature tags</label> | |
| 37 </param> | |
| 38 <param name="value" size="4" type="text" value="*"> | |
| 39 <label>Tag values</label> | |
| 40 </param> | |
| 41 <param name="join" type="select"> | |
| 42 <label>Join features</label> | |
| 43 <option value="no">No</option> | |
| 44 <option value="yes">Yes</option> | |
| 45 </param> | |
| 46 <param name="featinname" type="select"> | |
| 47 <label>Put feature type in sequence name</label> | |
| 48 <option value="no">No</option> | |
| 49 <option value="yes">Yes</option> | |
| 50 </param> | |
| 51 <param name="describe" size="4" type="text" value=""> | |
| 52 <label>Specify one or more tag names that should be added to the output sequence Description text</label> | |
| 53 </param> | |
| 54 <param name="out_format1" type="select"> | |
| 55 <label>Output Sequence File Format</label> | |
| 56 <option value="fasta">FASTA (m)</option> | |
| 57 <option value="acedb">ACeDB (m)</option> | |
| 58 <option value="asn1">ASN.1 (m)</option> | |
| 59 <option value="clustal">Clustal (m)</option> | |
| 60 <option value="codata">CODATA (m)</option> | |
| 61 <option value="embl">EMBL (m)</option> | |
| 62 <option value="fitch">Fitch (m)</option> | |
| 63 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option> | |
| 64 <option value="genbank">GENBANK (m)</option> | |
| 65 <option value="gff">GFF (m)</option> | |
| 66 <option value="hennig86">Hennig86 (m)</option> | |
| 67 <option value="ig">Intelligenetics (m)</option> | |
| 68 <option value="jackknifer">Jackknifer (m)</option> | |
| 69 <option value="jackknifernon">Jackknifernon (m)</option> | |
| 70 <option value="mega">Mega (m)</option> | |
| 71 <option value="meganon">Meganon (m)</option> | |
| 72 <option value="msf">Wisconsin Package GCG's MSF (m)</option> | |
| 73 <option value="pir">NBRF (PIR) (m)</option> | |
| 74 <option value="ncbi">NCBI style FASTA (m)</option> | |
| 75 <option value="nexus">Nexus/PAUP (m)</option> | |
| 76 <option value="nexusnon">Nexusnon/PAUPnon (m)</option> | |
| 77 <option value="phylip">PHYLIP interleaved (m)</option> | |
| 78 <option value="phylipnon">PHYLIP non-interleaved (m)</option> | |
| 79 <option value="selex">SELEX (m)</option> | |
| 80 <option value="staden">Staden (s)</option> | |
| 81 <option value="strider">DNA strider (m)</option> | |
| 82 <option value="swiss">SwisProt entry (m)</option> | |
| 83 <option value="text">Plain sequence (s)</option> | |
| 84 <option value="treecon">Treecon (m)</option> | |
| 85 </param> | |
| 86 </inputs> | |
| 87 <outputs> | |
| 88 <data format="fasta" name="out_file1" /> | |
| 89 </outputs> | |
| 90 <code file="emboss_format_corrector.py" /> | |
| 91 <help> | |
| 92 You can view the original documentation here_. | |
| 93 | |
| 94 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/extractfeat.html | |
| 95 </help> | |
| 96 </tool> |