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author yating-l
date Thu, 28 Jun 2018 12:36:33 -0400
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1 <tool id="blastXmlToPsl" name="blastXmlToPsl" version="1.1">
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2 <requirements>
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3 </requirements>
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4 <stdio>
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5 <exit_code range="1:" />
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6 </stdio>
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7 <command><![CDATA[
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8 $__tool_directory__/blastXmlToPsl $input $output
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9 #if $convertToNucCoords == "true"
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10 -convertToNucCoords
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11 #end if
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12 ]]></command>
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13 <inputs>
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14 <param type="data" name="input" format="xml" />
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15 <param type="boolean" name="convertToNucCoords" checked="true" label="-convertToNucCoords" help="Only support for TBLASTN restuls. Convert protein to nucleic alignments to nucleic
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16 to nucleic coordinates"/>
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17 </inputs>
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18 <outputs>
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19 <data format="psl" name="output" />
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="input" value="tblastn_Dbia3_ci.xml" />
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24 <param name="convertToNucCoords" value="true" />
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25 <output name="output" value="tblastn_Dbia3_ci.psl" />
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26 </test>
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27 <test>
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28 <param name="input" value="blastn_mRNA_seq.xml" />
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29 <param name="convertToNucCoords" value="false" />
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30 <output name="output" value="blastn_mRNA_seq.psl" />
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31 </test>
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32 </tests>
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33 <help><![CDATA[
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34 blastXmlToPsl - convert blast XML output to PSLs
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35
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36 usage:
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37 blastXmlToPsl [options] blastXml psl
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38
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39 options:
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40 -scores=file - Write score information to this file. Format is:
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41 strands qName qStart qEnd tName tStart tEnd bitscore eVal qDef tDef
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42
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43 -verbose=n - n >= 3 prints each line of file after parsing.
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44 n >= 4 dumps the result of each query
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45
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46 -eVal=n n is e-value threshold to filter results. Format can be either
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47 an integer, double or 1e-10. Default is no filter.
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48
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49 -pslx - create PSLX output (includes sequences for blocks)
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50
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51 -convertToNucCoords - convert protein to nucleic alignments to nucleic
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52 to nucleic coordinates
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53
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54 -qName=src - define element used to obtain the qName. The following
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55 values are support:
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56 - query-ID - use contents of the <Iteration_query-ID> element if it
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57 exists, otherwise use <BlastOutput_query-ID>
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58 - query-def0 - use the first white-space separated word of the
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59 <Iteration_query-def> element if it exists, otherwise the first word
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60 of <BlastOutput_query-def>.
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61
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62 Default is query-def0.
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63
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64 -tName=src - define element used to obtain the tName. The following
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65 values are support:
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66 - Hit_id - use contents of the <Hit-id> element.
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67 - Hit_def0 - use the first white-space separated word of the
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68 <Hit_def> element.
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69 - Hit_accession - contents of the <Hit_accession> element.
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70
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71 Default is Hit-def0.
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72
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73 -forcePsiBlast - treat as output of PSI-BLAST. blast-2.2.16 and maybe
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74 others indentify psiblast as blastp.
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75
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76 Output only results of last round from PSI BLAST
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77 ]]></help>
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78 <citations>
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79 <citation type="bibtex">
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80 @article{Kent01062002,
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81 author = {Kent, W. James and Sugnet, Charles W. and Furey, Terrence S. and Roskin, Krishna M. and Pringle, Tom H. and Zahler, Alan M. and Haussler, and David},
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82 title = {The Human Genome Browser at UCSC},
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83 volume = {12},
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84 number = {6},
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85 pages = {996-1006},
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86 year = {2002},
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87 doi = {10.1101/gr.229102},
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88 URL = {http://genome.cshlp.org/content/12/6/996.abstract},
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89 eprint = {http://genome.cshlp.org/content/12/6/996.full.pdf+html},
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90 journal = {Genome Research}
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91 }
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92 </citation>
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93 </citations>
0
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94 </tool>