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