Mercurial > repos > artbio > blastparser_and_hits
annotate BlastParser_and_hits.xml @ 0:9dfb65ebb02e draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
author | artbio |
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date | Sun, 15 Oct 2017 18:43:37 -0400 |
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children | 9beb85dba280 |
rev | line source |
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9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.5.0"> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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2 <description>for virus discovery</description> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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3 <requirements></requirements> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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4 <command><![CDATA[ |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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5 python '$__tool_directory__'/BlastParser_and_hits.py |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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6 --sequences '$sequences' |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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7 --blast '$blast' |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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8 --tabularOutput '$tabularOutput' |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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9 --fastaOutput '$fastaOutput' |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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10 --flanking $flanking |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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11 --mode $mode |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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12 ## Additional parameters. |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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13 #if $additional_filters.use_filters == "yes": |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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14 --filter_relativeCov $additional_filters.filter_relativeCov |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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15 --filter_maxScore $additional_filters.filter_maxScore |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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16 --filter_meanScore $additional_filters.filter_meanScore |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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17 --filter_term_in "$additional_filters.filter_term_in" |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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18 --filter_term_out "$additional_filters.filter_term_out" |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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19 #end if |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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20 --al_sequences '$al_sequences' |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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21 --un_sequences '$un_sequences' |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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22 --dataset_name "$blast.element_identifier" |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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23 |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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24 ]]></command> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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25 <inputs> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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26 <param name="sequences" type="data" format="fasta" label="fasta sequences that have been blasted" /> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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27 <param name="blast" type="data" format="tabular" label="The blast output you wish to parse"> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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28 <validator type="expression" message="Blast file must have 13 columns">value.metadata.columns == 13</validator> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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29 </param> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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30 <param name="flanking" type="integer" value= "5" label="Number of flanking nucleotides to add to hits for CAP3 assembly"/> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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31 <param name="mode" type="select" label="Extensive or compact reporting mode" help="display (extensive) or not (compact) the oases contigs"> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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32 <option value="verbose" selected="true">extensive</option> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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33 <option value="short">compact</option> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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34 </param> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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35 <conditional name="additional_filters"> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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36 <param name="use_filters" type="select" label="Use Additional Filters?"> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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37 <option value="no">No</option> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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38 <option value="yes">Yes</option> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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39 </param> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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40 <when value="no"> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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41 </when> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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42 <when value="yes"> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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43 <param name="filter_relativeCov" type="float" value="0" max="1" label="Minimum Relative Subject Coverage" help=""/> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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44 <param name="filter_maxScore" type="float" value="0" label="Minimum maximum BitScore" help=""/> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
artbio
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45 <param name="filter_meanScore" type="float" value="0" label="Minimum mean BitScore" help=""/> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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46 <param name="filter_term_in" type="text" value="" label="filter the subject list with a keyword" help=""/> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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47 <param name="filter_term_out" type="text" value="" label="filter the subject list excluding a keyword" help=""/> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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48 </when> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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49 </conditional> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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50 </inputs> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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51 <outputs> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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52 <data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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53 <data name="fastaOutput" format="fasta" label="hits"/> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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54 <data name="al_sequences" format="fasta" label="Blast aligned sequences"/> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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55 <data name="un_sequences" format="fasta" label="Blast unaligned sequences"/> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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56 </outputs> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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57 |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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58 <tests> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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59 <test> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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60 <param ftype="fasta" name="sequences" value="input.fa" /> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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61 <param ftype="tabular" name="blast" value="blast.tab" /> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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62 <param name="flanking" value="5" /> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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63 <param name="use_filters" value="no" /> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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64 <param name="mode" value="verbose" /> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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65 <output name="tabularOutput" ftype="tabular" file="output.tab" /> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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66 <output name="fastaOutput" ftype="fasta" file="output.fa" /> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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67 <output name="al_sequences" ftype="fasta" file="al_sequences.fa" /> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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68 <output name="un_sequences" ftype="fasta" file="un_sequences.fa" /> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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69 </test> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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70 </tests> |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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71 |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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72 <help> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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73 |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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74 **What it does** |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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75 |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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76 Parse blast output for viruses genome assembly. |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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77 |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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78 Takes as inputs |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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79 |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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80 - 1. the fasta sequences that have been submitted to blast |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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81 - 2. a blast alignment in a tabular format. **Importantly** this tabular output must contains the 12 standard columns (see blast documentation), **plus a column 13** that will report the length of the subject sequence (slen). When you use blast tools prior using this tool, remember to **check the appropriate box** to get the 13th column in the blast tabular output. |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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82 - 3. the numbers of flanking nucleotides to be recovered at the ends of blast hit sequences |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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83 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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84 The tool returns 4 datasets |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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85 |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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86 - 1. the fasta input sequences that produced significant blast hits |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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87 - 2. the fasta sequences that did not produced significant blast hits |
9dfb65ebb02e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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88 - 3. the sequences of the blast hits, plus the flanking sequences (as specified in the tool form). This dataset may be further used in metavisitor workflows to produce contigs of hits. |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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89 - 4. and the parsing of the blast alignments which summarizes the blast results by "subject" sequences (blast analysis, by subjects) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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90 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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91 This latter parsing dataset may be customized by tuning the reporting mode and/or using filters |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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92 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 48132e5edac97d54804ccbaf620068a5fb800bdc
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93 </help> |
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94 </tool> |