Mercurial > repos > drosofff > msp_blastparser_and_hits

annotate BlastParser_and_hits.xml @ 5:a941981a298c draft

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author drosofff
date Mon, 29 Jun 2015 08:36:19 -0400
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children 3f7cfa1cf90c
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1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.2.0">
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2 <description>for virus discovery</description>
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3 <requirements></requirements>
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4 <command interpreter="python">
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5 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 #end if
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18
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19 </command>
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20 <inputs>
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21 <param name="sequences" type="data" format="fasta" label="fasta sequences that have been blasted" />
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22 <param name="blast" type="data" format="tabular" label="The blast output you wish to parse" />
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23 <param name="flanking" type="text" size="5" value= "5" label="Number of flanking nucleotides to add to hits for CAP3 assembly"/>
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24 <param name="mode" type="select" label="Verbose or short reporting mode" help="display or not the oases contigs">
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25 <option value="verbose" default="true">verbose</option>
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26 <option value="short">do not report oases contigs</option>
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27 </param>
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28 <conditional name="additional_filters">
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29 <param name="use_filters" type="select" label="Use Additional Filters?">
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30 <option value="no">No</option>
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31 <option value="yes">Yes</option>
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32 </param>
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33 <when value="no">
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34 </when>
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35 <when value="yes">
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36 <param name="filter_relativeCov" type="float" value="0" max="1" label="Minimum Relative Subject Coverage" help=""/>
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37 <param name="filter_maxScore" type="float" value="0" label="Minimum maximum BitScore" help=""/>
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38 <param name="filter_meanScore" type="float" value="0" label="Minimum mean BitScore" help=""/>
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39 </when>
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40 </conditional>
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41 </inputs>
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42 <outputs>
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43 <data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/>
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44 <data name="fastaOutput" format="fasta" label="hits"/>
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45 </outputs>
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46
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47 <tests>
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48 <test>
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49 <param ftype="fasta" name="sequences" value="input.fa" />
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50 <param ftype="tabular" name="blast" value="blast.tab" />
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51 <param name="flanking" value="5" />
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52 <param name="use_filters" value="no" />
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53 <param name="mode" value="verbose" />
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54 <output name="tabularOutput" ftype="tabular" file="output.tab" />
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55 <output name="fastaOutput" ftype="fasta" file="output.fa" />
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56 </test>
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57 </tests>
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58
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59 <help>
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60
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61 **What it does**
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62
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63 Parse blast outputs for viruses genome assembly. Outputs analysis and hit sequences for further assembly
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64
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65 </help>
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66 </tool>