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annotate test-data/blastn_arabidopsis.xml @ 11:4c4a0da938ff draft

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Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. Supports $GALAXY_SLOTS. Includes more tests and heavy use of macros.
author peterjc
date Thu, 05 Dec 2013 06:55:59 -0500
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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1 <?xml version="1.0"?>
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2 <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
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3 <BlastOutput>
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4 <BlastOutput_program>blastn</BlastOutput_program>
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5 <BlastOutput_version>BLASTN 2.2.28+</BlastOutput_version>
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6 <BlastOutput_reference>Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), &quot;A greedy algorithm for aligning DNA sequences&quot;, J Comput Biol 2000; 7(1-2):203-14.</BlastOutput_reference>
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7 <BlastOutput_db>/mnt/galaxy/galaxy-central/database/files/000/dataset_857_files/blastdb</BlastOutput_db>
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8 <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
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9 <BlastOutput_query-def>chunk_of_plant</BlastOutput_query-def>
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10 <BlastOutput_query-len>630</BlastOutput_query-len>
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11 <BlastOutput_param>
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12 <Parameters>
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13 <Parameters_expect>0.001</Parameters_expect>
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14 <Parameters_sc-match>1</Parameters_sc-match>
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15 <Parameters_sc-mismatch>-2</Parameters_sc-mismatch>
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16 <Parameters_gap-open>0</Parameters_gap-open>
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17 <Parameters_gap-extend>0</Parameters_gap-extend>
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18 <Parameters_filter>L;m;</Parameters_filter>
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19 </Parameters>
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20 </BlastOutput_param>
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21 <BlastOutput_iterations>
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22 <Iteration>
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23 <Iteration_iter-num>1</Iteration_iter-num>
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24 <Iteration_query-ID>Query_1</Iteration_query-ID>
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25 <Iteration_query-def>chunk_of_plant</Iteration_query-def>
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26 <Iteration_query-len>630</Iteration_query-len>
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27 <Iteration_hits>
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28 <Hit>
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29 <Hit_num>1</Hit_num>
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30 <Hit_id>gnl|BL_ORD_ID|2</Hit_id>
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31 <Hit_def>chrIII gi|240255695|ref|NC_003074.8| Arabidopsis thaliana chromosome 3, complete sequence</Hit_def>
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32 <Hit_accession>2</Hit_accession>
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33 <Hit_len>23459830</Hit_len>
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34 <Hit_hsps>
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35 <Hsp>
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36 <Hsp_num>1</Hsp_num>
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37 <Hsp_bit-score>1164.51</Hsp_bit-score>
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38 <Hsp_score>630</Hsp_score>
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39 <Hsp_evalue>0</Hsp_evalue>
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40 <Hsp_query-from>1</Hsp_query-from>
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41 <Hsp_query-to>630</Hsp_query-to>
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42 <Hsp_hit-from>4341</Hsp_hit-from>
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43 <Hsp_hit-to>4970</Hsp_hit-to>
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44 <Hsp_query-frame>1</Hsp_query-frame>
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45 <Hsp_hit-frame>1</Hsp_hit-frame>
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46 <Hsp_identity>630</Hsp_identity>
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47 <Hsp_positive>630</Hsp_positive>
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48 <Hsp_gaps>0</Hsp_gaps>
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49 <Hsp_align-len>630</Hsp_align-len>
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50 <Hsp_qseq>GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT</Hsp_qseq>
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51 <Hsp_hseq>GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT</Hsp_hseq>
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52 <Hsp_midline>||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</Hsp_midline>
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53 </Hsp>
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54 </Hit_hsps>
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55 </Hit>
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56 </Iteration_hits>
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57 <Iteration_stat>
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58 <Statistics>
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59 <Statistics_db-num>5</Statistics_db-num>
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60 <Statistics_db-len>119146348</Statistics_db-len>
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61 <Statistics_hsp-len>26</Statistics_hsp-len>
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62 <Statistics_eff-space>71964315672</Statistics_eff-space>
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63 <Statistics_kappa>0.46</Statistics_kappa>
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64 <Statistics_lambda>1.28</Statistics_lambda>
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65 <Statistics_entropy>0.85</Statistics_entropy>
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66 </Statistics>
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67 </Iteration_stat>
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68 </Iteration>
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69 </BlastOutput_iterations>
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70 </BlastOutput>
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71