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author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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1 <tool id="EMBOSS: water107" name="water" version="5.0.0">
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2 <description>Smith-Waterman local alignment</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command>water -asequence $input1 -bsequence $input2 -outfile $out_file1 -gapopen "$gapopen" -gapextend "$gapextend" -brief $brief -aformat3 $out_format1 -auto</command>
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5 <inputs>
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6 <param format="fasta" name="input1" type="data">
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7 <label>Sequence 1</label>
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8 </param>
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9 <param format="fasta" name="input2" type="data">
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10 <label>Sequence 2</label>
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11 </param>
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12 <param name="gapopen" type="text" value="10.0">
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13 <label>Gap open penalty</label>
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14 </param>
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15 <param name="gapextend" type="text" value="0.5">
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16 <label>Gap extension penalty</label>
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17 </param>
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18 <param name="brief" type="select">
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19 <label>Brief identity and similarity</label>
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20 <option value="yes">Yes</option>
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21 <option value="no">No</option>
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22 </param>
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23 <param name="out_format1" type="select">
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24 <label>Output Alignment File Format</label>
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25 <option value="srs">SRS (m)</option>
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26 <option value="simple">Simple (m)</option>
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27 <option value="fasta">FASTA (m)</option>
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28 <option value="msf">MSF (m)</option>
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29 <option value="pair">Pair (p)</option>
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30 <option value="markx0">Markx0 (p)</option>
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31 <option value="markx1">Markx1 (p)</option>
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32 <option value="markx2">Markx2 (p)</option>
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33 <option value="markx3">Markx3 (p)</option>
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34 <option value="markx10">Markx10 (p)</option>
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35 <option value="srspair">SRS pair (p)</option>
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36 <option value="score">Score (p)</option>
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37 </param>
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38 </inputs>
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39 <outputs>
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40 <data format="srs" name="out_file1" />
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="input1" value="2.fasta"/>
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45 <param name="input2" value="1.fasta"/>
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46 <param name="gapopen" value="10.0"/>
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47 <param name="gapextend" value="0.5"/>
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48 <param name="brief" value="no"/>
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49 <param name="out_format1" value="score"/>
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50 <output name="out_file1" file="emboss_water_out.score"/>
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51 </test>
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52 </tests>
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53 <code file="emboss_format_corrector.py" />
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54 <help>
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55
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56 .. class:: warningmark
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57
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58 The input datasets need to be sequences.
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59
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60 -----
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61
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62 You can view the original documentation here_.
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63
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64 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/water.html
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65
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66 ------
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67
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68 **Citation**
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69
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70 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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71
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72 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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73 </help>
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74 </tool>