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1 <tool id="edu.tamu.cpt.blastp_to_gff3" name="BlastP Results to GFF3" version="19.1.0.0">
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2 <description>converts blast xml results to a JBrowse-compatible file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>cpt-macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 $__tool_directory__/blast_to_gff3.py
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10 $input_type.blast_input
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11 #if $input_type.input_type_selector == "xml":
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12 --blastxml
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13 $input_type.include_seq
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14 #elif $input_type.input_type_selector == "tsv":
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15 --blasttab
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16 #end if
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17 > $output]]></command>
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18 <inputs>
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19 <conditional name="input_type">
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20 <param name = "input_type_selector" type="select" label="Choose BlastP File Format">
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21 <option value="xml" selected="true">BlastXML</option>
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22 <option value="tsv">Blast 25 Column Table"</option>
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23 </param>
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24 <when value="xml">
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25 <param name="blast_input" type="data" format="xml" label="BlastXML Input"/>
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26 <param name="include_seq" type="boolean" label="Include protein alignment in Blast view in Apollo/JBrowse" truevalue="--include_seq" falsevalue="" />
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27 </when>
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28 <when value="tsv">
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29 <param name="blast_input" type="data" format="tabular" label="Blast 25 Column Table"/>
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30 </when>
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31 </conditional>
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32 </inputs>
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33 <outputs>
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34 <data format="gff3" name="output"/>
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="input_type_selector" value="xml"/>
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39 <param name="blast_input" value="BlastpXmlToGff_In.blastxml" ftype="xml"/>
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40 <param name="include_seq" value="false"/>
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41 <output name="output" file="BlastpXmlToGff_Out.gff3" ftype="gff3"/>
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42 </test>
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43 <test>
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44 <param name="input_type_selector" value="xml"/>
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45 <param name="blast_input" value="BlastpXmlToGff_In.blastxml" ftype="xml"/>
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46 <param name="include_seq" value="true"/>
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47 <output name="output" file="BlastpXmlToGff_OutWithSeq.gff3" ftype="gff3"/>
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48 </test>
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49 <test>
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50 <param name="input_type_selector" value="tsv"/>
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51 <param name="blast_input" value="BlastpTabToGff_In.tabular" ftype="tabular"/>
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52 <param name="include_seq" value="false"/>
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53 <output name="output" ftype="gff3">
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54 <assert_contents>
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55 <has_line line="##gff-version 3"/>
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56 <has_n_lines n="122"/>
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57 </assert_contents>
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58 </output>
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59 </test>
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60 </tests>
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61 <help><![CDATA[
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62 **What it does**
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63
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64 Convert BlastP XML or tabular results into GFF3 format for visualization within JBrowse, please be sure to select the correct input option for your data.
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65 This is critical for displaying the position of high-scoring pairs of the Target aligned against the Query. If you need to convert BlastN results, please use the "BlastN Results to GFF3" tool.
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66
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67 **Options::**
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68
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69 By selecting **Include protein alignment…**, the actual sequence alignment will be displayed
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70 in the pop-up BLAST view in Apollo/JBrowse. This option currently only works when using XML input.
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71
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72 ]]></help>
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73 <expand macro="citations" />
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74 </tool>
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75
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