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diff 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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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastn_arabidopsis.xml	Thu Dec 05 06:55:59 2013 -0500
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+<?xml version="1.0"?>
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
+<BlastOutput>
+  <BlastOutput_program>blastn</BlastOutput_program>
+  <BlastOutput_version>BLASTN 2.2.28+</BlastOutput_version>
+  <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>
+  <BlastOutput_db>/mnt/galaxy/galaxy-central/database/files/000/dataset_857_files/blastdb</BlastOutput_db>
+  <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
+  <BlastOutput_query-def>chunk_of_plant</BlastOutput_query-def>
+  <BlastOutput_query-len>630</BlastOutput_query-len>
+  <BlastOutput_param>
+    <Parameters>
+      <Parameters_expect>0.001</Parameters_expect>
+      <Parameters_sc-match>1</Parameters_sc-match>
+      <Parameters_sc-mismatch>-2</Parameters_sc-mismatch>
+      <Parameters_gap-open>0</Parameters_gap-open>
+      <Parameters_gap-extend>0</Parameters_gap-extend>
+      <Parameters_filter>L;m;</Parameters_filter>
+    </Parameters>
+  </BlastOutput_param>
+<BlastOutput_iterations>
+<Iteration>
+  <Iteration_iter-num>1</Iteration_iter-num>
+  <Iteration_query-ID>Query_1</Iteration_query-ID>
+  <Iteration_query-def>chunk_of_plant</Iteration_query-def>
+  <Iteration_query-len>630</Iteration_query-len>
+<Iteration_hits>
+<Hit>
+  <Hit_num>1</Hit_num>
+  <Hit_id>gnl|BL_ORD_ID|2</Hit_id>
+  <Hit_def>chrIII gi|240255695|ref|NC_003074.8| Arabidopsis thaliana chromosome 3, complete sequence</Hit_def>
+  <Hit_accession>2</Hit_accession>
+  <Hit_len>23459830</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>1164.51</Hsp_bit-score>
+      <Hsp_score>630</Hsp_score>
+      <Hsp_evalue>0</Hsp_evalue>
+      <Hsp_query-from>1</Hsp_query-from>
+      <Hsp_query-to>630</Hsp_query-to>
+      <Hsp_hit-from>4341</Hsp_hit-from>
+      <Hsp_hit-to>4970</Hsp_hit-to>
+      <Hsp_query-frame>1</Hsp_query-frame>
+      <Hsp_hit-frame>1</Hsp_hit-frame>
+      <Hsp_identity>630</Hsp_identity>
+      <Hsp_positive>630</Hsp_positive>
+      <Hsp_gaps>0</Hsp_gaps>
+      <Hsp_align-len>630</Hsp_align-len>
+      <Hsp_qseq>GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT</Hsp_qseq>
+      <Hsp_hseq>GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT</Hsp_hseq>
+      <Hsp_midline>||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>5</Statistics_db-num>
+      <Statistics_db-len>119146348</Statistics_db-len>
+      <Statistics_hsp-len>26</Statistics_hsp-len>
+      <Statistics_eff-space>71964315672</Statistics_eff-space>
+      <Statistics_kappa>0.46</Statistics_kappa>
+      <Statistics_lambda>1.28</Statistics_lambda>
+      <Statistics_entropy>0.85</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+</Iteration>
+</BlastOutput_iterations>
+</BlastOutput>
+