Mercurial > repos > rmarenco > blastxmltopsl

changeset 0:d5c3e461f484 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/remimarenco/blastXmlToPsl commit 748d4887ce50f21d581c973686a4c2f9eaa29cad-dirty
author rmarenco
date Thu, 14 Jul 2016 17:45:34 -0400
parents
children 5e8fd7791c7f
files README.md blastXmlToPsl.xml test-data/tblastn_Dbia3_ci.xml tool_dependencies.xml
diffstat 4 files changed, 351 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Thu Jul 14 17:45:34 2016 -0400
@@ -0,0 +1,11 @@
+Galaxy wrapper for blastXmlToPsl
+--------------------------------
+
+Converts blast XML output to PSLs
+
+This tool is configured only to use this command, at the moment:
+- blastXmlToPsl -convertToNucCoords $input $output
+
+Please use another tool or contact me
+
+(Contains blastXmlToPsl binary for [linux.x86_64](http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blastXmlToPsl.xml	Thu Jul 14 17:45:34 2016 -0400
@@ -0,0 +1,20 @@
+<tool id="blastXmlToPsl" name="blastXmlToPsl" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="1.0">blastXmlToPsl</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+        blastXmlToPsl -convertToNucCoords $input $output
+    ]]></command>
+    <inputs>
+        <param type="data" name="input" format="xml" />
+    </inputs>
+    <outputs>
+        <data format="psl" name="output" />
+    </outputs>
+    <help><![CDATA[
+        blastXmlToPsl - convert blast XML output to PSLs
+    ]]></help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tblastn_Dbia3_ci.xml	Thu Jul 14 17:45:34 2016 -0400
@@ -0,0 +1,297 @@
+<?xml version="1.0"?>
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
+<BlastOutput>
+  <BlastOutput_program>tblastn</BlastOutput_program>
+  <BlastOutput_version>TBLASTN 2.2.30+</BlastOutput_version>
+  <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
+  <BlastOutput_db>Dbia3.fa</BlastOutput_db>
+  <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
+  <BlastOutput_query-def>ci-PA FBpp0088245</BlastOutput_query-def>
+  <BlastOutput_query-len>1397</BlastOutput_query-len>
+  <BlastOutput_param>
+    <Parameters>
+      <Parameters_matrix>BLOSUM62</Parameters_matrix>
+      <Parameters_expect>0.01</Parameters_expect>
+      <Parameters_gap-open>11</Parameters_gap-open>
+      <Parameters_gap-extend>1</Parameters_gap-extend>
+      <Parameters_filter>L;</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>ci-PA FBpp0088245</Iteration_query-def>
+  <Iteration_query-len>1397</Iteration_query-len>
+<Iteration_hits>
+<Hit>
+  <Hit_num>1</Hit_num>
+  <Hit_id>gnl|BL_ORD_ID|0</Hit_id>
+  <Hit_def>contig1</Hit_def>
+  <Hit_accession>0</Hit_accession>
+  <Hit_len>45179</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>852.818</Hsp_bit-score>
+      <Hsp_score>2202</Hsp_score>
+      <Hsp_evalue>0</Hsp_evalue>
+      <Hsp_query-from>576</Hsp_query-from>
+      <Hsp_query-to>1396</Hsp_query-to>
+      <Hsp_hit-from>31367</Hsp_hit-from>
+      <Hsp_hit-to>33826</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>-2</Hsp_hit-frame>
+      <Hsp_identity>540</Hsp_identity>
+      <Hsp_positive>627</Hsp_positive>
+      <Hsp_gaps>39</Hsp_gaps>
+      <Hsp_align-len>840</Hsp_align-len>
+      <Hsp_qseq>KPYICKAPGCTKRYTDPSSLRKHVKTVHGAEFYANKKHKGLPLNDANSRLQQNNS--RHNLQEHNIDSSPCSEDSHLGKMLGTXXXXXXXXXXXXXXNHHLVNGVRASDSLLTYSPDDLAEXXXXXXXXXXXXXXXXXXXXXXXRAMVNIGNGNASASTIGGSVLARQRFRGRLQTKGINSSTIMLCNIPESNRTFGISELNQRITELKMEPGTDAEIKIPKLPNTTIGGYTEDPLQNQTSFRNTVSNKQG--TVSGSIQGQFRRDSQNSTASTYYGXXXXXXXXXXXXXXXIPTMRPNPSCN-STASFYDPISPGCSRRSSQMSNGANCNSFTSTSGLPVLNKE--SNKSLNACINKPNIGVQGVGIYNXXXXXXXXXHLIATNLKRLQRKDSE--YHNFTSGRFSVPSYMHSLHIKNNKPVGENEFDKAIASNA-RRQTDPVPNINLDPLTNISRFSTTPHSFDINVGKTN--NIASSINKDNLRKDLFTVSIKADMAMTSDQHPNERINLDEVEELILPDEMLQYLNLVKDDTNHLEKEHQAVPVGSNVSETIASNH--YREQSNIYYTNKQILTPPSNVDI----QPNTTKFTVQDKFAMTAVGGSFSQRELSTLAVPNEHGHAKCESFHHQSQKYMNTDIGSKQQSALPSAHQRQTEKSNYNQIIDSSMTSLPELNVDSIYPRNETENIFKVHGDHDNEIQCGIISQSQMSPSTNLNNDGQFSTVNMQPITTSKLF-PPEPQKIVCDTQASNTSVMHLDTYQRTLEYVQSCQNWMETNNTSTNQIQSLPGMPVNNTLFPDVSSSTHPYHGTNMVINDMTTSLTSLLEENRYLQMM</Hsp_qseq>
+      <Hsp_hseq>KPYICKAPGCTKRYTDPSSLRKHVKTVHGAEFYANKKHKGLPLNDANSRLHRDSGQGRHNLQEHNIDSSPCSEELQVGKLIGMSSPSIKSESDESSPHHQLLSGVRASDCFLTYSQDGAAEHITLDDGWDCDDDVDVADLPIVLRAMVNVGSGNSMAPTIGGGVVARQRFRSRLQTKGINSSMVMLGNIPESNRTIGISELNQRITELKMEPGTACDITVPL--NTGLERISEDLSQNQS---NITLNKQSFFTASGSLQGHFRRDSQNSTASTYYGSMQSRRSSQSSQVSSISTMRPGPSYNTTTASLYDPISPGCSRRSSQMSNVVNSYALTSTSGLTAINKDLNANSSPNASINKPGLGGQYFGFYNNSLPPPPSSHLIATNLKHLQDTDSRSCYHNTTGGRFSIPNCTPSLHLDYNGPAGEQEIDKEIPNNILRRQSEPMPNISLDTLTNVSPLSGPLQNLQFPIGKARNVNITSSSNENTLRKGPCHATMKTEMTMTSEQHPNERINLDEVEELILPDEMLQYLNLVKDDQNYMEKDD--VAIRSTVPKTIKSNENLLLSKSNLNPIKKQIILPTSNFDVSINLQPNTSNLQTQEEHTMTTIGGLPSQREQN--IVPHQHEKTKCRSFPQEIDKTINIDIGFKEQPYPSSAYQPQITKSNQNEIIDSSMTSLPELN--PIFTKINSENVSKLHRDQNSEIQCGIVSQSQMSPSININNDGETSTLKNLPLTYSKFSGQPNTQTTVG---GSNTSSMVSDTYQRTLEYVQSCQNWVDTNNSSGDQIQS------NNTLWSDVSSSTHPYAGTNLVINDMTTSLTSLLEENRYLHMM</Hsp_hseq>
+      <Hsp_midline>KPYICKAPGCTKRYTDPSSLRKHVKTVHGAEFYANKKHKGLPLNDANSRL +++   RHNLQEHNIDSSPCSE+  +GK++G SSPSIKSESD SS +H L++GVRASD  LTYS D  AE++ LDDGW+CDDDVDVADLPIVLRAMVN+G+GN+ A TIGG V+ARQRFR RLQTKGINSS +ML NIPESNRT GISELNQRITELKMEPGT  +I +P   NT +   +ED  QNQ+   N   NKQ   T SGS+QG FRRDSQNSTASTYYGSMQSRRSSQSSQVSSI TMRP PS N +TAS YDPISPGCSRRSSQMSN  N  + TSTSGL  +NK+  +N S NA INKP +G Q  G YN+SLPPPPSSHLIATNLK LQ  DS   YHN T GRFS+P+   SLH+  N P GE E DK I +N  RRQ++P+PNI+LD LTN+S  S    +    +GK    NI SS N++ LRK     ++K +M MTS+QHPNERINLDEVEELILPDEMLQYLNLVKDD N++EK+   V + S V +TI SN      +SN+    KQI+ P SN D+    QPNT+    Q++  MT +GG  SQRE +   VP++H   KC SF  +  K +N DIG K+Q    SA+Q Q  KSN N+IIDSSMTSLPELN   I+ +  +EN+ K+H D ++EIQCGI+SQSQMSPS N+NNDG+ ST+   P+T SK    P  Q  V     SNTS M  DTYQRTLEYVQSCQNW++TNN+S +QIQS      NNTL+ DVSSSTHPY GTN+VINDMTTSLTSLLEENRYL MM</Hsp_midline>
+    </Hsp>
+    <Hsp>
+      <Hsp_num>2</Hsp_num>
+      <Hsp_bit-score>604.749</Hsp_bit-score>
+      <Hsp_score>1558</Hsp_score>
+      <Hsp_evalue>0</Hsp_evalue>
+      <Hsp_query-from>14</Hsp_query-from>
+      <Hsp_query-to>520</Hsp_query-to>
+      <Hsp_hit-from>34107</Hsp_hit-from>
+      <Hsp_hit-to>35765</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>-1</Hsp_hit-frame>
+      <Hsp_identity>395</Hsp_identity>
+      <Hsp_positive>432</Hsp_positive>
+      <Hsp_gaps>48</Hsp_gaps>
+      <Hsp_align-len>554</Hsp_align-len>
+      <Hsp_qseq>YSELQFLXXXXXXXXXXXXTVLPGSPCINQHHXXXXXXXXXXXXXXXXGGTSDSIKTS--IQPQICNENTLLGNA-GXXXXXXXXXXXXXXVTGQPH--DFHPAYRIPGYMEQLYSLQRTNSASSFH------------------------DPYVNCASAFHLAGLGLGSADFXXXXXXXXXXELHNXXXXXXXXGSLASTDFHFSVDGNRRLGSPRPPGGSIRASISRKRALSSSPYSDSFDINSMIRFSPNSLATIMNXXXXXXXXXXXXXXXXXTALNPMSHVHSTRLQQIQAHLLRASAGLLNPMTPQQVAASGFSIGHMPTSASLRVNDVHPNLSDSHIQITTSPTVTKDVSQVPAAAFSL------------------KNLDDAREKKGPFKDVVPEQPSSTSGGVAQVEADSASSQLSDRCYNNVVNNITGIPGDVKVNSRLDEYINCGSISIPSNEYDCANADTTDIKDEPGDFIETNCHWRSCRIEFITQDELVKHINNDHIQTNKKAFVCRWEDCTRGEKPFKAQYMLVVHMRRHTGEKPHKCT</Hsp_qseq>
+      <Hsp_hseq>YSELQFLASRRAAAVAAAATVLPVSPCINHVHTTDVSSSVTVPSMIQTVEASDSIKTATTIQPPICNGNTLLANSTGHHQNHQGQHVHSLNVTGQPHAHEFHPAYRIPGYMEQLYSLQRNGSTTSFHGIVFLCHYT*CPY*TFTYQYL*FLDPYVNCASAFHLAGLGLGSGDFLGTRGMGSLGDLHHAAVAAAAAGSLASTDFHFSIDGNRRLSSPRPPGGSIRASISRKRALSSSPYSDSFDINSMIRFSPNSLATIMNGSRGSSAASGSYGHISASAINPISHAHSTLAPRLQ-HLLRASAGLLNPMNTQQAAAAGFSISHAASAAALSLNDVHGNLNDLPGQITPSSTARLVADEHKMAALSVI*NCLIKSYILFI*CF*QKDFNDGNQRNRQRKSTVTEQPSSTSGSVAQVEADSASSHLSDRCYNNIASTTKSIVGDVKTSRRCEDFISSGSASTPLNEYDCANADTTDIKDEPGDFIETNCHWRSCCIEFNTQDELVKHINNDHIQTNKKAFVCRWENCTRGEKPFKAQYMLVVHMRRHTGEKPHKCT</Hsp_hseq>
+      <Hsp_midline>YSELQFLASRRAAAVAAAATVLP SPCIN  H TDVSSSVTVPS+I T   SDSIKT+  IQP ICN NTLL N+ GH  NHQ QHVH++NVTGQPH  +FHPAYRIPGYMEQLYSLQR  S +SFH                        DPYVNCASAFHLAGLGLGS DFLG+RG+ SLG+LH+AAVAAAAAGSLASTDFHFS+DGNRRL SPRPPGGSIRASISRKRALSSSPYSDSFDINSMIRFSPNSLATIMNGSRGSSAASGSYGHISA+A+NP+SH HST   ++Q HLLRASAGLLNPM  QQ AA+GFSI H  ++A+L +NDVH NL+D   QIT S T      +   AA S+                  K+ +D  ++    K  V EQPSSTSG VAQVEADSASS LSDRCYNN+ +    I GDVK + R +++I+ GS S P NEYDCANADTTDIKDEPGDFIETNCHWRSC IEF TQDELVKHINNDHIQTNKKAFVCRWE+CTRGEKPFKAQYMLVVHMRRHTGEKPHKCT</Hsp_midline>
+    </Hsp>
+    <Hsp>
+      <Hsp_num>3</Hsp_num>
+      <Hsp_bit-score>119.398</Hsp_bit-score>
+      <Hsp_score>298</Hsp_score>
+      <Hsp_evalue>0</Hsp_evalue>
+      <Hsp_query-from>521</Hsp_query-from>
+      <Hsp_query-to>575</Hsp_query-to>
+      <Hsp_hit-from>33880</Hsp_hit-from>
+      <Hsp_hit-to>34044</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>-3</Hsp_hit-frame>
+      <Hsp_identity>54</Hsp_identity>
+      <Hsp_positive>54</Hsp_positive>
+      <Hsp_gaps>0</Hsp_gaps>
+      <Hsp_align-len>55</Hsp_align-len>
+      <Hsp_qseq>FEGCFKAYSRLENLKTHLRSHTGEKPYTCEYPGCSKAFSNASDRAKHQNRTHSNE</Hsp_qseq>
+      <Hsp_hseq>FEGCFKAYSRLENLKTHLRSHTGEKPYMCEYPGCSKAFSNASDRAKHQNRTHSNE</Hsp_hseq>
+      <Hsp_midline>FEGCFKAYSRLENLKTHLRSHTGEKPY CEYPGCSKAFSNASDRAKHQNRTHSNE</Hsp_midline>
+    </Hsp>
+    <Hsp>
+      <Hsp_num>4</Hsp_num>
+      <Hsp_bit-score>33.4982</Hsp_bit-score>
+      <Hsp_score>75</Hsp_score>
+      <Hsp_evalue>0.0015721</Hsp_evalue>
+      <Hsp_query-from>1</Hsp_query-from>
+      <Hsp_query-to>13</Hsp_query-to>
+      <Hsp_hit-from>41471</Hsp_hit-from>
+      <Hsp_hit-to>41509</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>-2</Hsp_hit-frame>
+      <Hsp_identity>13</Hsp_identity>
+      <Hsp_positive>13</Hsp_positive>
+      <Hsp_gaps>0</Hsp_gaps>
+      <Hsp_align-len>13</Hsp_align-len>
+      <Hsp_qseq>MDAYALPTYFPLA</Hsp_qseq>
+      <Hsp_hseq>MDAYALPTYFPLA</Hsp_hseq>
+      <Hsp_midline>MDAYALPTYFPLA</Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>1</Statistics_db-num>
+      <Statistics_db-len>45179</Statistics_db-len>
+      <Statistics_hsp-len>66</Statistics_hsp-len>
+      <Statistics_eff-space>19955683</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>2</Iteration_iter-num>
+  <Iteration_query-ID>Query_2</Iteration_query-ID>
+  <Iteration_query-def>ci-PC FBpp0300417</Iteration_query-def>
+  <Iteration_query-len>572</Iteration_query-len>
+<Iteration_hits>
+<Hit>
+  <Hit_num>1</Hit_num>
+  <Hit_id>gnl|BL_ORD_ID|0</Hit_id>
+  <Hit_def>contig1</Hit_def>
+  <Hit_accession>0</Hit_accession>
+  <Hit_len>45179</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>616.69</Hsp_bit-score>
+      <Hsp_score>1589</Hsp_score>
+      <Hsp_evalue>0</Hsp_evalue>
+      <Hsp_query-from>14</Hsp_query-from>
+      <Hsp_query-to>553</Hsp_query-to>
+      <Hsp_hit-from>33879</Hsp_hit-from>
+      <Hsp_hit-to>35765</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>-1</Hsp_hit-frame>
+      <Hsp_identity>416</Hsp_identity>
+      <Hsp_positive>454</Hsp_positive>
+      <Hsp_gaps>91</Hsp_gaps>
+      <Hsp_align-len>630</Hsp_align-len>
+      <Hsp_qseq>YSELQFLXXXXXXXXXXXXTVLPGSPCINQHHXXXXXXXXXXXXXXXXGGTSDSIKT--SIQPQICNENTLLGNA-GXXXXXXXXXXXXXXVTGQPH--DFHPAYRIPGYMEQLYSLQRTNSASSFH------------------------DPYVNCASAFHLAGLGLGSADFXXXXXXXXXXELHNXXXXXXXXGSLASTDFHFSVDGNRRLGSPRPPGGSIRASISRKRALSSSPYSDSFDINSMIRFSPNSLATIMNXXXXXXXXXXXXXXXXXTALNPMSHVHSTRLQQIQAHLLRASAGLLNPMTPQQVAASGFSIGHMPTSASLRVNDVHPNLSDSHIQITTSPTVTKDVSQVPAAAFSL------------------KNLDDAREKKGPFKDVVPEQPSSTSGGVAQVEADSASSQLSDRCYNNVVNNITGIPGDVKVNSRLDEYINCGSISIPSNEYDCANADTTDIKDEPGDFIETNCHWRSCRIEFITQDELVKHINNDHIQTNKKAFVCRWEDCTRGEKPFKAQYMLVVHMRRHTGEKPHKCT-------------------------------------------EKNHTLASIRDVAKPLVMLVIAQSIKIEHTVMR</Hsp_qseq>
+      <Hsp_hseq>YSELQFLASRRAAAVAAAATVLPVSPCINHVHTTDVSSSVTVPSMIQTVEASDSIKTATTIQPPICNGNTLLANSTGHHQNHQGQHVHSLNVTGQPHAHEFHPAYRIPGYMEQLYSLQRNGSTTSFHGIVFLCHYT*CPY*TFTYQYL*FLDPYVNCASAFHLAGLGLGSGDFLGTRGMGSLGDLHHAAVAAAAAGSLASTDFHFSIDGNRRLSSPRPPGGSIRASISRKRALSSSPYSDSFDINSMIRFSPNSLATIMNGSRGSSAASGSYGHISASAINPISHAHSTLAPRLQ-HLLRASAGLLNPMNTQQAAAAGFSISHAASAAALSLNDVHGNLNDLPGQITPSSTARLVADEHKMAALSVI*NCLIKSYILFI*CF*QKDFNDGNQRNRQRKSTVTEQPSSTSGSVAQVEADSASSHLSDRCYNNIASTTKSIVGDVKTSRRCEDFISSGSASTPLNEYDCANADTTDIKDEPGDFIETNCHWRSCCIEFNTQDELVKHINNDHIQTNKKAFVCRWENCTRGEKPFKAQYMLVVHMRRHTGEKPHKCTVRLLLFKIFDFQA*LIVIVFSLKAVLRHIHAWKT*KHIYGHTQVKNPICASIRDAARRLVMQAIVQSIKIVLTVMR</Hsp_hseq>
+      <Hsp_midline>YSELQFLASRRAAAVAAAATVLP SPCIN  H TDVSSSVTVPS+I T   SDSIKT  +IQP ICN NTLL N+ GH  NHQ QHVH++NVTGQPH  +FHPAYRIPGYMEQLYSLQR  S +SFH                        DPYVNCASAFHLAGLGLGS DFLG+RG+ SLG+LH+AAVAAAAAGSLASTDFHFS+DGNRRL SPRPPGGSIRASISRKRALSSSPYSDSFDINSMIRFSPNSLATIMNGSRGSSAASGSYGHISA+A+NP+SH HST   ++Q HLLRASAGLLNPM  QQ AA+GFSI H  ++A+L +NDVH NL+D   QIT S T      +   AA S+                  K+ +D  ++    K  V EQPSSTSG VAQVEADSASS LSDRCYNN+ +    I GDVK + R +++I+ GS S P NEYDCANADTTDIKDEPGDFIETNCHWRSC IEF TQDELVKHINNDHIQTNKKAFVCRWE+CTRGEKPFKAQYMLVVHMRRHTGEKPHKCT                                            KN   ASIRD A+ LVM  I QSIKI  TVMR</Hsp_midline>
+    </Hsp>
+    <Hsp>
+      <Hsp_num>2</Hsp_num>
+      <Hsp_bit-score>42.3578</Hsp_bit-score>
+      <Hsp_score>98</Hsp_score>
+      <Hsp_evalue>1.2328e-06</Hsp_evalue>
+      <Hsp_query-from>490</Hsp_query-from>
+      <Hsp_query-to>572</Hsp_query-to>
+      <Hsp_hit-from>33769</Hsp_hit-from>
+      <Hsp_hit-to>34056</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>-3</Hsp_hit-frame>
+      <Hsp_identity>37</Hsp_identity>
+      <Hsp_positive>47</Hsp_positive>
+      <Hsp_gaps>13</Hsp_gaps>
+      <Hsp_align-len>96</Hsp_align-len>
+      <Hsp_qseq>DCTRGEKPFKAQYML---VVHMRRHTGEKPHKCTEK--NHTLASIRDVAKPLVML----VIAQSIKIEHTV----MRNRTFVKHLDAQNVTPTRAL</Hsp_qseq>
+      <Hsp_hseq>DCF*FEGCFKAYSRLENLKTHLRSHTGEKPYMCEYPGCSKAFSNASDRAKHQNRTHSNEVSAQPSSNKNNL*LKSFRNRTFVKLLVARNVTPTQVL</Hsp_hseq>
+      <Hsp_midline>DC   E  FKA   L     H+R HTGEKP+ C     +   ++  D AK         V AQ    ++ +     RNRTFVK L A+NVTPT+ L</Hsp_midline>
+    </Hsp>
+    <Hsp>
+      <Hsp_num>3</Hsp_num>
+      <Hsp_bit-score>30.8018</Hsp_bit-score>
+      <Hsp_score>68</Hsp_score>
+      <Hsp_evalue>0.00386248</Hsp_evalue>
+      <Hsp_query-from>1</Hsp_query-from>
+      <Hsp_query-to>13</Hsp_query-to>
+      <Hsp_hit-from>41471</Hsp_hit-from>
+      <Hsp_hit-to>41509</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>-2</Hsp_hit-frame>
+      <Hsp_identity>13</Hsp_identity>
+      <Hsp_positive>13</Hsp_positive>
+      <Hsp_gaps>0</Hsp_gaps>
+      <Hsp_align-len>13</Hsp_align-len>
+      <Hsp_qseq>MDAYALPTYFPLA</Hsp_qseq>
+      <Hsp_hseq>MDAYALPTYFPLA</Hsp_hseq>
+      <Hsp_midline>MDAYALPTYFPLA</Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>1</Statistics_db-num>
+      <Statistics_db-len>45179</Statistics_db-len>
+      <Statistics_hsp-len>60</Statistics_hsp-len>
+      <Statistics_eff-space>7679488</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>3</Iteration_iter-num>
+  <Iteration_query-ID>Query_3</Iteration_query-ID>
+  <Iteration_query-def>ci-PB FBpp0297298</Iteration_query-def>
+  <Iteration_query-len>1279</Iteration_query-len>
+<Iteration_hits>
+<Hit>
+  <Hit_num>1</Hit_num>
+  <Hit_id>gnl|BL_ORD_ID|0</Hit_id>
+  <Hit_def>contig1</Hit_def>
+  <Hit_accession>0</Hit_accession>
+  <Hit_len>45179</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>855.514</Hsp_bit-score>
+      <Hsp_score>2209</Hsp_score>
+      <Hsp_evalue>0</Hsp_evalue>
+      <Hsp_query-from>458</Hsp_query-from>
+      <Hsp_query-to>1278</Hsp_query-to>
+      <Hsp_hit-from>31367</Hsp_hit-from>
+      <Hsp_hit-to>33826</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>-2</Hsp_hit-frame>
+      <Hsp_identity>540</Hsp_identity>
+      <Hsp_positive>627</Hsp_positive>
+      <Hsp_gaps>39</Hsp_gaps>
+      <Hsp_align-len>840</Hsp_align-len>
+      <Hsp_qseq>KPYICKAPGCTKRYTDPSSLRKHVKTVHGAEFYANKKHKGLPLNDANSRLQQNNS--RHNLQEHNIDSSPCSEDSHLGKMLGTXXXXXXXXXXXXXXNHHLVNGVRASDSLLTYSPDDLAEXXXXXXXXXXXXXXXXXXXXXXXRAMVNIGNGNASASTIGGSVLARQRFRGRLQTKGINSSTIMLCNIPESNRTFGISELNQRITELKMEPGTDAEIKIPKLPNTTIGGYTEDPLQNQTSFRNTVSNKQG--TVSGSIQGQFRRDSQNSTASTYYGXXXXXXXXXXXXXXXIPTMRPNPSCN-STASFYDPISPGCSRRSSQMSNGANCNSFTSTSGLPVLNKE--SNKSLNACINKPNIGVQGVGIYNXXXXXXXXXHLIATNLKRLQRKDSE--YHNFTSGRFSVPSYMHSLHIKNNKPVGENEFDKAIASNA-RRQTDPVPNINLDPLTNISRFSTTPHSFDINVGKTN--NIASSINKDNLRKDLFTVSIKADMAMTSDQHPNERINLDEVEELILPDEMLQYLNLVKDDTNHLEKEHQAVPVGSNVSETIASNH--YREQSNIYYTNKQILTPPSNVDI----QPNTTKFTVQDKFAMTAVGGSFSQRELSTLAVPNEHGHAKCESFHHQSQKYMNTDIGSKQQSALPSAHQRQTEKSNYNQIIDSSMTSLPELNVDSIYPRNETENIFKVHGDHDNEIQCGIISQSQMSPSTNLNNDGQFSTVNMQPITTSKLF-PPEPQKIVCDTQASNTSVMHLDTYQRTLEYVQSCQNWMETNNTSTNQIQSLPGMPVNNTLFPDVSSSTHPYHGTNMVINDMTTSLTSLLEENRYLQMM</Hsp_qseq>
+      <Hsp_hseq>KPYICKAPGCTKRYTDPSSLRKHVKTVHGAEFYANKKHKGLPLNDANSRLHRDSGQGRHNLQEHNIDSSPCSEELQVGKLIGMSSPSIKSESDESSPHHQLLSGVRASDCFLTYSQDGAAEHITLDDGWDCDDDVDVADLPIVLRAMVNVGSGNSMAPTIGGGVVARQRFRSRLQTKGINSSMVMLGNIPESNRTIGISELNQRITELKMEPGTACDITVPL--NTGLERISEDLSQNQS---NITLNKQSFFTASGSLQGHFRRDSQNSTASTYYGSMQSRRSSQSSQVSSISTMRPGPSYNTTTASLYDPISPGCSRRSSQMSNVVNSYALTSTSGLTAINKDLNANSSPNASINKPGLGGQYFGFYNNSLPPPPSSHLIATNLKHLQDTDSRSCYHNTTGGRFSIPNCTPSLHLDYNGPAGEQEIDKEIPNNILRRQSEPMPNISLDTLTNVSPLSGPLQNLQFPIGKARNVNITSSSNENTLRKGPCHATMKTEMTMTSEQHPNERINLDEVEELILPDEMLQYLNLVKDDQNYMEKDD--VAIRSTVPKTIKSNENLLLSKSNLNPIKKQIILPTSNFDVSINLQPNTSNLQTQEEHTMTTIGGLPSQREQN--IVPHQHEKTKCRSFPQEIDKTINIDIGFKEQPYPSSAYQPQITKSNQNEIIDSSMTSLPELN--PIFTKINSENVSKLHRDQNSEIQCGIVSQSQMSPSININNDGETSTLKNLPLTYSKFSGQPNTQTTVG---GSNTSSMVSDTYQRTLEYVQSCQNWVDTNNSSGDQIQS------NNTLWSDVSSSTHPYAGTNLVINDMTTSLTSLLEENRYLHMM</Hsp_hseq>
+      <Hsp_midline>KPYICKAPGCTKRYTDPSSLRKHVKTVHGAEFYANKKHKGLPLNDANSRL +++   RHNLQEHNIDSSPCSE+  +GK++G SSPSIKSESD SS +H L++GVRASD  LTYS D  AE++ LDDGW+CDDDVDVADLPIVLRAMVN+G+GN+ A TIGG V+ARQRFR RLQTKGINSS +ML NIPESNRT GISELNQRITELKMEPGT  +I +P   NT +   +ED  QNQ+   N   NKQ   T SGS+QG FRRDSQNSTASTYYGSMQSRRSSQSSQVSSI TMRP PS N +TAS YDPISPGCSRRSSQMSN  N  + TSTSGL  +NK+  +N S NA INKP +G Q  G YN+SLPPPPSSHLIATNLK LQ  DS   YHN T GRFS+P+   SLH+  N P GE E DK I +N  RRQ++P+PNI+LD LTN+S  S    +    +GK    NI SS N++ LRK     ++K +M MTS+QHPNERINLDEVEELILPDEMLQYLNLVKDD N++EK+   V + S V +TI SN      +SN+    KQI+ P SN D+    QPNT+    Q++  MT +GG  SQRE +   VP++H   KC SF  +  K +N DIG K+Q    SA+Q Q  KSN N+IIDSSMTSLPELN   I+ +  +EN+ K+H D ++EIQCGI+SQSQMSPS N+NNDG+ ST+   P+T SK    P  Q  V     SNTS M  DTYQRTLEYVQSCQNW++TNN+S +QIQS      NNTL+ DVSSSTHPY GTN+VINDMTTSLTSLLEENRYL MM</Hsp_midline>
+    </Hsp>
+    <Hsp>
+      <Hsp_num>2</Hsp_num>
+      <Hsp_bit-score>529.25</Hsp_bit-score>
+      <Hsp_score>1362</Hsp_score>
+      <Hsp_evalue>0</Hsp_evalue>
+      <Hsp_query-from>1</Hsp_query-from>
+      <Hsp_query-to>402</Hsp_query-to>
+      <Hsp_hit-from>34107</Hsp_hit-from>
+      <Hsp_hit-to>35435</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>-1</Hsp_hit-frame>
+      <Hsp_identity>310</Hsp_identity>
+      <Hsp_positive>341</Hsp_positive>
+      <Hsp_gaps>43</Hsp_gaps>
+      <Hsp_align-len>444</Hsp_align-len>
+      <Hsp_qseq>MEQLYSLQRTNSASSFH------------------------DPYVNCASAFHLAGLGLGSADFXXXXXXXXXXELHNXXXXXXXXGSLASTDFHFSVDGNRRLGSPRPPGGSIRASISRKRALSSSPYSDSFDINSMIRFSPNSLATIMNXXXXXXXXXXXXXXXXXTALNPMSHVHSTRLQQIQAHLLRASAGLLNPMTPQQVAASGFSIGHMPTSASLRVNDVHPNLSDSHIQITTSPTVTKDVSQVPAAAFSL------------------KNLDDAREKKGPFKDVVPEQPSSTSGGVAQVEADSASSQLSDRCYNNVVNNITGIPGDVKVNSRLDEYINCGSISIPSNEYDCANADTTDIKDEPGDFIETNCHWRSCRIEFITQDELVKHINNDHIQTNKKAFVCRWEDCTRGEKPFKAQYMLVVHMRRHTGEKPHKCT</Hsp_qseq>
+      <Hsp_hseq>MEQLYSLQRNGSTTSFHGIVFLCHYT*CPY*TFTYQYL*FLDPYVNCASAFHLAGLGLGSGDFLGTRGMGSLGDLHHAAVAAAAAGSLASTDFHFSIDGNRRLSSPRPPGGSIRASISRKRALSSSPYSDSFDINSMIRFSPNSLATIMNGSRGSSAASGSYGHISASAINPISHAHSTLAPRLQ-HLLRASAGLLNPMNTQQAAAAGFSISHAASAAALSLNDVHGNLNDLPGQITPSSTARLVADEHKMAALSVI*NCLIKSYILFI*CF*QKDFNDGNQRNRQRKSTVTEQPSSTSGSVAQVEADSASSHLSDRCYNNIASTTKSIVGDVKTSRRCEDFISSGSASTPLNEYDCANADTTDIKDEPGDFIETNCHWRSCCIEFNTQDELVKHINNDHIQTNKKAFVCRWENCTRGEKPFKAQYMLVVHMRRHTGEKPHKCT</Hsp_hseq>
+      <Hsp_midline>MEQLYSLQR  S +SFH                        DPYVNCASAFHLAGLGLGS DFLG+RG+ SLG+LH+AAVAAAAAGSLASTDFHFS+DGNRRL SPRPPGGSIRASISRKRALSSSPYSDSFDINSMIRFSPNSLATIMNGSRGSSAASGSYGHISA+A+NP+SH HST   ++Q HLLRASAGLLNPM  QQ AA+GFSI H  ++A+L +NDVH NL+D   QIT S T      +   AA S+                  K+ +D  ++    K  V EQPSSTSG VAQVEADSASS LSDRCYNN+ +    I GDVK + R +++I+ GS S P NEYDCANADTTDIKDEPGDFIETNCHWRSC IEF TQDELVKHINNDHIQTNKKAFVCRWE+CTRGEKPFKAQYMLVVHMRRHTGEKPHKCT</Hsp_midline>
+    </Hsp>
+    <Hsp>
+      <Hsp_num>3</Hsp_num>
+      <Hsp_bit-score>119.398</Hsp_bit-score>
+      <Hsp_score>298</Hsp_score>
+      <Hsp_evalue>0</Hsp_evalue>
+      <Hsp_query-from>403</Hsp_query-from>
+      <Hsp_query-to>457</Hsp_query-to>
+      <Hsp_hit-from>33880</Hsp_hit-from>
+      <Hsp_hit-to>34044</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>-3</Hsp_hit-frame>
+      <Hsp_identity>54</Hsp_identity>
+      <Hsp_positive>54</Hsp_positive>
+      <Hsp_gaps>0</Hsp_gaps>
+      <Hsp_align-len>55</Hsp_align-len>
+      <Hsp_qseq>FEGCFKAYSRLENLKTHLRSHTGEKPYTCEYPGCSKAFSNASDRAKHQNRTHSNE</Hsp_qseq>
+      <Hsp_hseq>FEGCFKAYSRLENLKTHLRSHTGEKPYMCEYPGCSKAFSNASDRAKHQNRTHSNE</Hsp_hseq>
+      <Hsp_midline>FEGCFKAYSRLENLKTHLRSHTGEKPY CEYPGCSKAFSNASDRAKHQNRTHSNE</Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>1</Statistics_db-num>
+      <Statistics_db-len>45179</Statistics_db-len>
+      <Statistics_hsp-len>66</Statistics_hsp-len>
+      <Statistics_eff-space>18186509</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+</Iteration>
+</BlastOutput_iterations>
+</BlastOutput>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jul 14 17:45:34 2016 -0400
@@ -0,0 +1,23 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <!-- Package blastXmlToPsl -->
+    <package name="blastXmlToPsl" version="1.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_binary" target_directory="bin">
+                    <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/blastXmlToPsl
+                    </url_template>
+                    <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/blastXmlToPsl
+                    </url_template>
+                </action>
+                <action type="chmod">
+                    <file mode="750">$INSTALL_DIR/bin/blastXmlToPsl</file>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
+    </package>
+</tool_dependency>
\ No newline at end of file