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author drosofff
date Wed, 11 Oct 2017 12:43:04 -0400
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1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.4.4">
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2 <description>for virus discovery</description>
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3 <requirements></requirements>
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4 <command><![CDATA[
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5 python '$__tool_directory__'/BlastParser_and_hits.py
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6 --sequences '$sequences'
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7 --blast '$blast'
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8 --tabularOutput '$tabularOutput'
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9 --fastaOutput '$fastaOutput'
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10 --flanking $flanking
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11 --mode $mode
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12 ## Additional parameters.
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13 #if $additional_filters.use_filters == "yes":
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14 --filter_relativeCov $additional_filters.filter_relativeCov
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15 --filter_maxScore $additional_filters.filter_maxScore
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16 --filter_meanScore $additional_filters.filter_meanScore
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17 --filter_term_in "$additional_filters.filter_term_in"
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18 --filter_term_out "$additional_filters.filter_term_out"
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19 #end if
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20 --al_sequences '$al_sequences'
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21 --un_sequences '$un_sequences'
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22 --dataset_name "$blast.element_identifier"
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23
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24 ]]></command>
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25 <inputs>
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26 <param name="sequences" type="data" format="fasta" label="fasta sequences that have been blasted" />
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27 <param name="blast" type="data" format="tabular" label="The blast output you wish to parse">
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28 <validator type="expression" message="Blast file must have 13 columns">value.metadata.columns == 13</validator>
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29 </param>
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30 <param name="flanking" type="integer" value= "5" label="Number of flanking nucleotides to add to hits for CAP3 assembly"/>
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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">
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32 <option value="verbose" selected="true">extensive</option>
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33 <option value="short">compact</option>
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34 </param>
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35 <conditional name="additional_filters">
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36 <param name="use_filters" type="select" label="Use Additional Filters?">
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37 <option value="no">No</option>
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38 <option value="yes">Yes</option>
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39 </param>
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40 <when value="no">
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41 </when>
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42 <when value="yes">
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43 <param name="filter_relativeCov" type="float" value="0" max="1" label="Minimum Relative Subject Coverage" help=""/>
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44 <param name="filter_maxScore" type="float" value="0" label="Minimum maximum BitScore" help=""/>
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45 <param name="filter_meanScore" type="float" value="0" label="Minimum mean BitScore" help=""/>
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46 <param name="filter_term_in" type="text" value="" label="filter the subject list with a keyword" help=""/>
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47 <param name="filter_term_out" type="text" value="" label="filter the subject list excluding a keyword" help=""/>
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48 </when>
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49 </conditional>
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50 </inputs>
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51 <outputs>
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52 <data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/>
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53 <data name="fastaOutput" format="fasta" label="hits"/>
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54 <data name="al_sequences" format="fasta" label="Blast aligned sequences"/>
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55 <data name="un_sequences" format="fasta" label="Blast unaligned sequences"/>
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56 </outputs>
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57
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58 <tests>
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59 <test>
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60 <param ftype="fasta" name="sequences" value="input.fa" />
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61 <param ftype="tabular" name="blast" value="blast.tab" />
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62 <param name="flanking" value="5" />
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63 <param name="use_filters" value="no" />
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64 <param name="mode" value="verbose" />
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65 <output name="tabularOutput" ftype="tabular" file="output.tab" />
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66 <output name="fastaOutput" ftype="fasta" file="output.fa" />
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67 <output name="al_sequences" ftype="fasta" file="al_sequences.fa" />
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68 <output name="un_sequences" ftype="fasta" file="un_sequences.fa" />
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69 </test>
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70 </tests>
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71
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72 <help>
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73
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74 **What it does**
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75
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76 Parse blast output for viruses genome assembly.
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78 Takes as inputs
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80 - 1. the fasta sequences that have been submitted to blast
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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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82 - 3. the numbers of flanking nucleotides to be recovered at the ends of blast hit sequences
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83
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84 The tool returns 4 datasets
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85
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86 - 1. the fasta input sequences that produced significant blast hits
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87 - 2. the fasta sequences that did not produced significant blast hits
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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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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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90
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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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92
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93 </help>
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94 </tool>