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1 <tool id="EMBOSS: kssearch" name="kssearch" version="1.0.2">
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2 <description>Search similar sequences in public repositories using SSEARCH</description>
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3 <command>kssearch -seqall $input1 -moltype $moltype -histogram $histogram -nucleotide $nucleotide -topstrand $topstrand -bottomstrand $bottomstrand -gapopen $gapopen -gapext $gapext -scores $scores -alignments $alignments -ktup $ktup -matrix $matrix -eupper $eupper -elower $elower -dbrange $dbrange -seqrange $seqrange -auto -outfile $out_file1</command>
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4 <inputs>
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5 <param format="data" name="input1" type="data">
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6 <label>Sequence</label>
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7 </param>
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8 <param name="moltype" size="4" type="text" value="">
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9 <label>molecular type</label>
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10 </param>
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11 <param name="histogram" type="select" value="">
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12 <label>Display histogram</label>
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13 <option value="no">No</option>
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14 <option value="yes">Yes</option>
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15 </param>
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16 <param name="nucleotide" type="select" value="">
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17 <label>your query is nucleotide or not(protein)</label>
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18 <option value="no">No</option>
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19 <option value="yes">Yes</option>
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20 </param>
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21 <param name="topstrand" type="select" value="">
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22 <label>Nucleotide sequence strand to use for seqrch (top)</label>
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23 <option value="no">No</option>
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24 <option value="yes">Yes</option>
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25 </param>
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26 <param name="bottomstrand" type="select" value="">
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27 <label>Nucleotide sequence strand to use for seqrch (bottom)</label>
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28 <option value="no">No</option>
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29 <option value="yes">Yes</option>
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30 </param>
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31 <param name="gapopen" size="4" type="integer" value="">
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32 <label>Score for the initiation of a gap</label>
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33 </param>
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34 <param name="gapext" size="4" type="integer" value="">
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35 <label>Score for each base/residue in a gap</label>
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36 </param>
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37 <param name="scores" size="4" type="integer" value="">
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38 <label>Maximum number of scores displayed in the output</label>
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39 </param>
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40 <param name="alignments" size="4" type="integer" value="">
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41 <label>Maximum number of alignments displayed in the output</label>
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42 </param>
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43 <param name="ktup" size="4" type="integer" value="">
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44 <label>Word size to use for sequence comparisons</label>
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45 </param>
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46 <param name="matrix" size="4" type="text" value="">
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47 <label>Scoring matrix to be used in the search</label>
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48 </param>
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49 <param name="eupper" size="4" type="float" value="">
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50 <label>Upper E-value threshold</label>
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51 </param>
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52 <param name="elower" size="4" type="float" value="">
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53 <label>Lower E-value threshold</label>
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54 </param>
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55 <param name="dbrange" size="4" type="text" value="">
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56 <label>Range of sequence lengths in search database to include in search</label>
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57 </param>
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58 <param name="seqrange" size="4" type="text" value="">
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59 <label>Region of the query sequence to use for the search</label>
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60 </param>
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61
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62 </inputs>
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63 <outputs>
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64 <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
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65 </outputs>
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66 </tool>
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