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1 <tool id="EMBOSS: kblast" name="kblast" version="1.0.2">
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2 <description>Search similar sequences in public repositories using BLAST</description>
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3 <command>kblast -seqall $input1 -database $database -program $program -server $server -format $format -eval $eval -qfilter $qfilter -opengap $opengap -extendgap $extendgap -dropoff $dropoff -penalty $penalty -reward $reward -numdescriptions $numdescriptions -numalignments $numalignments -threshold $threshold -g $g -matrix $matrix -wordsize $wordsize -dbsize $dbsize -k $k -searchsp $searchsp -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="database" size="4" type="text" value="swissprot">
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9 <label>database name about target for your search</label>
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10 </param>
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11 <param name="program" size="4" type="text" value="auto">
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12 <label>blast program name. 'auto' (infer suitable program from your sequence), 'blastn', 'blastp' or 'blastx'</label>
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13 </param>
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14 <param name="server" size="4" type="text" value="">
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15 <label>specify web server for your search. 'NCBI', 'EBI' or 'DDBJ'</label>
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16 </param>
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17 <param name="format" size="4" type="text" value="0">
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18 <label>blast report format. 0 : normal BLAST report 8 : tabulark 1: ID listk 2: ID list separated by conmma</label>
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19 </param>
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20 <param name="eval" size="4" type="text" value="10.0">
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21 <label>Expectation value</label>
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22 </param>
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23 <param name="qfilter" size="4" type="text" value="T">
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24 <label></label>
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25 </param>
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26 <param name="opengap" size="4" type="integer" value="-1">
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27 <label>cost to open a gap</label>
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28 </param>
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29 <param name="extendgap" size="4" type="integer" value="-1">
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30 <label>cost to extend a gap</label>
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31 </param>
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32 <param name="dropoff" size="4" type="text" value="0">
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33 <label>X dropoff value for gapped alignment (in bits)</label>
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34 </param>
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35 <param name="penalty" size="4" type="integer" value="-3">
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36 <label>penalty for a nucleotide mismatch (blastn only)</label>
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37 </param>
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38 <param name="reward" size="4" type="integer" value="1">
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39 <label>reward for a nucleotide match (blastn only)</label>
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40 </param>
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41 <param name="numdescriptions" size="4" type="integer" value="500">
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42 <label>show one-line descriptions for this number of database sequences</label>
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43 </param>
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44 <param name="numalignments" size="4" type="integer" value="250">
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45 <label>number of database sequence to show alignments for (B)</label>
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46 </param>
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47 <param name="threshold" size="4" type="integer" value="0">
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48 <label>threshold for extending hits, default if zero for each program</label>
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49 </param>
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50 <param name="g" type="select" value="no">
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51 <label>perform gapped alignment</label>
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52 <option value="no">No</option>
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53 <option value="yes">Yes</option>
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54 </param>
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55 <param name="matrix" size="4" type="text" value="BLOSUM62">
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56 <label>matrix</label>
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57 </param>
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58 <param name="wordsize" size="4" type="integer" value="0">
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59 <label>word size, default if zero for each program</label>
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60 </param>
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61 <param name="dbsize" size="4" type="float" value="0">
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62 <label>effective size of the database</label>
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63 </param>
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64 <param name="k" size="4" type="integer" value="0">
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65 <label>number of best hits from a region to keep</label>
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66 </param>
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67 <param name="searchsp" size="4" type="float" value="0">
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68 <label>effective length of the search space</label>
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69 </param>
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70
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71 </inputs>
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72 <outputs>
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73 <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
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74 </outputs>
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75 </tool>
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