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annotate blastxml_to_gapped_gff3.xml @ 0:bd47051afe98 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
author iuc
date Tue, 20 Dec 2016 09:21:11 -0500
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bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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1 <tool id="blastxml_to_gapped_gff3" name="BlastXML to gapped GFF3" version="1.1">
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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5 </macros>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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6 <expand macro="requirements"/>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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7 <expand macro="stdio"/>
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8 <version_command>python blastxml_to_gapped_gff3.py --version</version_command>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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9 <command>
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10 <![CDATA[
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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11 python '$__tool_directory__/blastxml_to_gapped_gff3.py'
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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12 '$blastxml'
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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13 --min_gap $min_gap
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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14 $trim
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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15 > '$output'
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16 ]]></command>
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17 <inputs>
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18 <param label="Blast XML" name="blastxml" type="data" format="blastxml"/>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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19 <param label="Maximum gap size before generating a new match_part" name="min_gap" type="integer" value="3"/>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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21 <param type="select" label="Trim sides of blast hits" name="trim">
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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22 <option value="">None</option>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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23 <option value="--trim">Trim start and end</option>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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24 <option value="--trim_end" selected="true">Trim only end</option>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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25 </param>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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26 </inputs>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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27 <outputs>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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28 <data format="gff3" name="output"/>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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29 </outputs>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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30 <tests>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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31 <test>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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32 <param name="blastxml" ftype="blastxml" value="input.xml"/>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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33 <output name="output" file="blast.gff"/>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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34 </test>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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35 </tests>
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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36 <help><![CDATA[
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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37 **What it does**
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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38
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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39 Convert BlastXML results into GFF3 format.
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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40
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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41 **Options**
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42
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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43 The trimming option captures an important feature provided in this tool that
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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44 isn't provided in most other BlastXML visualization tools: the fact that blast
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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45 captures complete alignment location information.
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46
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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47 This means that when most blast visualization tools produce output which looks
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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48 like this:
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49
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50 .. image:: $PATH_TO_IMAGES/blast2html.png
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51
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52 This tool produces output which shows where the real subject sequence starts and ends relative to your sequence:
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bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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54 .. image:: $PATH_TO_IMAGES/blast-extended.png
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bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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56 This can be a useful feature for examining alternate start locations that are
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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57 used by sequences found from your blast query.
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58
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59 The green bars on the very top row of the picture indicate start sites, as you
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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60 can see the blast hits and the genome in the visualization share an upstream
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61 start site. You don't lose the information present in your blastxml data.
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62
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63 So, to the end of useful functionality, this options is controllable:
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64
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65 - you can trim neither end, see where the real protein alignments are.
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66 - you can trim both ends, like blasts HTML reports
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67 - you can trim just the end of the sequence, as upstream is generally more
bd47051afe98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 commit 8f38145c94ecb1e23c3ff6f0243213dc49d2287e
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68 interesting, and having long tails can result in poor visualizations.
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69 ]]></help>
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70 <citations>
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71 </citations>
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72 </tool>
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73