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annotate blastXmlToPsl.xml @ 0:ed804cd92001 draft

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author yating-l
date Tue, 02 May 2017 13:21:49 -0400
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1 <tool id="blastXmlToPsl" name="blastXmlToPsl" version="0.1.0">
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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 -convertToNucCoords $input $output
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9 ]]></command>
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10 <inputs>
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11 <param type="data" name="input" format="xml" />
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12 </inputs>
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13 <outputs>
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14 <data format="psl" name="output" />
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15 </outputs>
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16 <help><![CDATA[
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17 blastXmlToPsl - convert blast XML output to PSLs
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18
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19 usage:
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20 blastXmlToPsl [options] blastXml psl
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21
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22 options:
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23 -scores=file - Write score information to this file. Format is:
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24 strands qName qStart qEnd tName tStart tEnd bitscore eVal qDef tDef
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25
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26 -verbose=n - n >= 3 prints each line of file after parsing.
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27 n >= 4 dumps the result of each query
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28
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29 -eVal=n n is e-value threshold to filter results. Format can be either
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30 an integer, double or 1e-10. Default is no filter.
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31
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32 -pslx - create PSLX output (includes sequences for blocks)
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33
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34 -convertToNucCoords - convert protein to nucleic alignments to nucleic
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35 to nucleic coordinates
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36
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37 -qName=src - define element used to obtain the qName. The following
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38 values are support:
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39 - query-ID - use contents of the <Iteration_query-ID> element if it
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40 exists, otherwise use <BlastOutput_query-ID>
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41 - query-def0 - use the first white-space separated word of the
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42 <Iteration_query-def> element if it exists, otherwise the first word
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43 of <BlastOutput_query-def>.
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44
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45 Default is query-def0.
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46
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47 -tName=src - define element used to obtain the tName. The following
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48 values are support:
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49 - Hit_id - use contents of the <Hit-id> element.
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50 - Hit_def0 - use the first white-space separated word of the
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51 <Hit_def> element.
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52 - Hit_accession - contents of the <Hit_accession> element.
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53
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54 Default is Hit-def0.
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55
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56 -forcePsiBlast - treat as output of PSI-BLAST. blast-2.2.16 and maybe
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57 others indentify psiblast as blastp.
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58
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59 Output only results of last round from PSI BLAST
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60 ]]></help>
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61 </tool>