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1 <tool id="extract_wrapper" name="Extract" version="0.2">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="3.02">glimmer</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 extract_wrapper.py --exSequence $exSequence --exCoords $exCoords
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8 #if $ex2Fields
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9 --ex2Fields
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10 #end if
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11 #if $exDir
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12 --exDir
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13 #end if
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14 #if str($exMinLen)
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15 --exMinLen=$exMinLen
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16 #end if
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17 #if $exNoStart
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18 --exNoStart
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19 #end if
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20 #if $exNoStop
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21 --exNoStop
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22 #end if
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23 #if $exNoWrap
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24 --exNoWrap
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25 #end if
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26 --exOutput $exOutput --logfile $logfile
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27 </command>
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28
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29 <inputs>
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30 <param name="exSequence" type="data" format="fasta" label="DNA sequence to be analyzed" help="FASTA format" />
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31
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32 <param name="exCoords" type="data" format="glimmer_coords" label="Coordinates produced by Long-ORFs" />
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33
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34 <param name="ex2Fields" type="boolean" checked="false" label="Output sequence in 2 fields (-2, --2_fields)" help="Output each sequence as 2 fields (tag and sequence) on a single line." />
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35
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36 <param name="exDir" type="boolean" checked="false" label="Specify sequence direction (-d, --dir)" help="Use the 4th column of each input line to specify the direction of the sequence. Positive is forward, negative is reverse. The input sequence is assumed to be circular." />
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37
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38 <param name="exMinLen" type="integer" value="" optional="true" label="Minimum length of sequence (-l, --minlen)" help="Don't output any sequence shorter than n characters." />
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39
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40 <param name="exNoStart" type="boolean" checked="false" label="Omit first characters (-s, --nostart)" help="Omit the first 3 characters of each output string." />
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41
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42 <param name="exNoStop" type="boolean" checked="false" label="Omit last characters (-t, --nostop)" help="Omit the last 3 characters of each output string." />
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43
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44 <param name="exNoWrap" type="boolean" checked="false" label="No wraparound (-w, --nowrap)" help="Use the actual input coordinates without any wraparound that would be needed by a circular genome. Without this option, the output sequence is the shorter of the two ways around the circle. Tick 'Specify sequence direction' to specify direction explicitly." />
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45 </inputs>
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46
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47 <outputs>
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48 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
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49 <data name="exOutput" format="fasta" label="${tool.name} on ${on_string}: output" />
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50 </outputs>
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51
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52 <tests>
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53
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54 </tests>
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55 <help>
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56 **What it does**
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57
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58 Read FASTA-format *sequence-file* and extract from it the subsequences specified by *coords*. By default, *coords* is the name of a file containing lines of the form *tag* *start* *stop* [*frame*] ...
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59 Coordinates are inclusive counting from 1, e.g. *1 3* represents the 1st 3 characters of the sequence. For each line the corresponding region of *sequence-file* is extracted and output (after reverse-complementing if necessary).
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60
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61
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62 **License and citation**
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63
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64 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
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65
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66 .. _CRS4 Srl.: http://www.crs4.it/
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67 .. _MIT license: http://opensource.org/licenses/MIT
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68
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69 If you use this tool in Galaxy, please cite |Cuccuru2013|_.
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70
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71 .. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted*
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72 .. _Cuccuru2013: http://orione.crs4.it/
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73
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74 This tool uses `Glimmer`_, which is licensed separately. Please cite |Delcher2007|_.
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75
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76 .. _Glimmer: http://ccb.jhu.edu/software/glimmer/index.shtml
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77 .. |Delcher2007| replace:: Delcher, A. L., Bratke, K. A., Powers, E. C., Salzberg, S. L. (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. *Bioinformatics* 23(6), 673-679
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78 .. _Delcher2007: http://bioinformatics.oxfordjournals.org/content/23/6/673
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79 </help>
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80 </tool>
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