Mercurial > repos > devteam > emboss_5

annotate emboss_extractfeat.xml @ 10:9b98d3d903c6 draft

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author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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10
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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" 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" 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" 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" 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" 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" 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" 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" 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" 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
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96 ------
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97
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98 **Citation**
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99
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100 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
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101
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102 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
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103 </help>
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104 </tool>