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1 <?xml version="1.0"?>
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2 <tool id="edu.tamu.cpt.gff3.promote_qualifiers" name="Promote Qualifers" version="20.0.0">
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3 <description>Promote a child feature's qualifier into the parent feature</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"><![CDATA[
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10 python $__tool_directory__/promote_qualifier.py
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11 @INPUT_GFF@
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12 $parent
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13 $child
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14 $qualifier
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15 > $output]]></command>
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16 <inputs>
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17 <expand macro="gff3_input" />
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18 <param label="Parent Feature Type" name="parent" type="text" help="e.g. gene, mRNA, exon" />
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19 <param label="Child Feature Type" name="child" type="text" help="e.g. mRNA, exon, CDS" />
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20 <param label="Qualifer to Promote" name="qualifier" type="text" help="e.g. Name, Product, Notes" />
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21 </inputs>
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22 <outputs>
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23 <data format="gff3" name="output" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="gff3_data" value="promote_qualifiers_in.gff3" />
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28 <param name="parent" value="gene" />
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29 <param name="child" value="mRNA" />
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30 <param name="qualifier" value="Name" />
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31 <output name="output" file="promote_qualifiers_out.gff3" />
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32 </test>
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33 </tests>
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34 <help><![CDATA[
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35 **What it does**
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36
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37 Allows you to copy a specified qualifier value from a child feature into a parent feature, most likely to copy the Name from an mRNA into a gene.
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38
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39 For example, for a *Parent Feature Type* of "gene", *Child Feature Type* of "mRNA", and *Qualifier to Promote* of "Name" the following gff will be changed (spacing for emphasis):
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40
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41 *Before*::
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42
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43 NC_049846.1 . gene 630 1182 . + . ID=8942304a;date_last_modified=2020-09-25; Name=NC_049846.1.gene_1 ;date_creation=2020-09-25
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44 NC_049846.1 . mRNA 630 1182 . + . Parent=8942304a;ID=536ddf54; Name=Gene_1_Name ;date_creation=2020-09-25
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45
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46 *After*::
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47
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48 NC_049846.1 . gene 630 1182 . + . ID=8942304a;date_last_modified=2020-09-25; Name=Gene_1_Name ;date_creation=2020-09-25
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49 NC_049846.1 . mRNA 630 1182 . + . Parent=8942304a;ID=536ddf54; Name=Gene_1_Name ;date_creation=2020-09-25
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50
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51 .. class:: infomark
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52
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53 **Notes**::
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54
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55 - If the qualifier is already present in the parent, it will be overwritten with the child's value.
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56 - If there are multiple child features of the specified type under the same parent, the value from the first child. This action is strand aware.
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57 - For positive strand features it will select the child with the smaller start coordinate.
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58 - For negative strand it will select the child with the largest end coordinate.
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59
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60 .. class:: warningmark
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61
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62 **Warning**::
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63
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64 You should likely never run this to promote the "ID" qualifier as this will break the gff3 hierarchy structure and cause parsing failures downstream.
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65 ]]></help>
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66 <expand macro="citations-clm" />
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67 </tool>
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