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1 <?xml version="1.0"?>
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2 <tool id="edu.tamu.cpt.blast.relatedness.prot" name="Related Genomes" version="19.1.0.0">
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3 <description>based on protein blast results</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <import>cpt-macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="aggressive">
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10 $__tool_directory__/relatedness_prot.py
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11 ${blastIn.blast}
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12 $__tool_directory__/TaxID_List.txt
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13 --hits $hits
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14 $filter
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15 --protein
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16 #if $blastIn.blastType == "XML":
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17 --xmlMode
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18 #end if
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19 --taxFilter "$taxFilter"
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20 > $accession_list
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21 </command>
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22 <inputs>
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23 <conditional name="blastIn">
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24 <param name="blastType" type="select" label="Blastn Input Type">
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25 <option value="XML" selected="true">Blast XML</option>
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26 <option value="TSV">Blast Tabular</option>
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27 </param>
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28 <when value="XML">
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29 <param label="Blastn Results (Blast XML)" name="blast" type="data" format="blastxml"/>
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30 </when>
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31 <when value="TSV">
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32 <param label="Blastn Results" name="blast" type="data" format="tsv,tabular"/>
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33 </when>
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34 </conditional>
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35 <param label = 'Number of results to return' name="hits" type="integer" size="15" value="5"/>
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36 <param name="filter" type="boolean" truevalue="" falsevalue="--noFilter" checked="true" label="Automatically filter by phage Taxonomy IDs"/>
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37 <param name="taxFilter" type="text" label="TaxIDs to filter out of results (Space separated)"/>
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38 </inputs>
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39 <outputs>
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40 <data format="tabular" name="accession_list" label="Top BlastP Hits" />
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41 </outputs>
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42 <tests>
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43 <test>
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44 <conditional name="blastIn">
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45 <param name="blastType" value="TSV"/>
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46 <param name="blast" value="prot_relate_in.tab"/>
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47 </conditional>
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48 <param name="hits" value="10"/>
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49 <output name="accession_list" file="prot_relate_out.tab" lines_diff="4"/>
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50 </test>
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51 </tests>
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52 <help>
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53 **What it does**
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54
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55 This tool filters a set of BLASTp results and return the top
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56 related genomes based on number of protein-protein matches. The
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57 default mode is to only consider phage hits (based on TaxID),
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58 but this can the toggled off.
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59
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60 The input must be a tabular file from a BLASTp run with the qseqID,
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61 sallseqid, salltitles, sallacc, and staxIDs fields selected.
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62
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63 The output will be a tabular file with the top hits returned,
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64 where each row specifies the TaxID, organism name, and number of
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65 similar unique protein hits shared.
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66 </help>
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67 <expand macro="citations-2020" />
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68 </tool>
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