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annotate intersect_and_adjacent.xml @ 2:0dbc7fbad0ab draft

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author cpt
date Mon, 12 Aug 2024 03:04:00 +0000
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1 <tool id="edu.tamu.cpt.gff3.intersect_and_adjacent" name="Intersect and Adjacent" version="21.0.0">
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2 <description>Outputs nearby top-level GFF features from two GFF3 files</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="3.0.2">intervaltree</requirement>
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8 </expand>
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9 <command detect_errors="aggressive"><![CDATA[
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10 python '$__tool_directory__/intersect_and_adjacent.py'
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11 '$gff3_data_a'
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12 '$gff3_data_b'
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13 '$window'
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14 '$stranding'
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15 --oa '$oa'
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16 --ob '$ob'
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param label="GFF3 Annotations A" name="gff3_data_a" type="data" format="gff3"/>
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21 <param label="GFF3 Annotations B" name="gff3_data_b" type="data" format="gff3"/>
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22 <param label="Adjacency Window Size" name="window" type="integer" value="0"/>
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23 <param label="Only allow adjacencies for features on the same strand" name="stranding" type="boolean" checked="false" truevalue="-stranding" falsevalue=""/>
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24 </inputs>
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25 <outputs>
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26 <data format="gff3" name="oa" label="GFF3 Annotations from ${gff3_data_a.name} in ${gff3_data_b.name}"/>
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27 <data format="gff3" name="ob" label="GFF3 Annotations from ${gff3_data_b.name} in ${gff3_data_a.name}"/>
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="gff3_data_a" value="T7_IntersectAIn.gff3"/>
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32 <param name="gff3_data_b" value="T7_IntersectBIn.gff3"/>
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33 <param name="window" value="50"/>
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34 <param name="stranding" value="-stranding"/>
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35 <output name="oa" file="T7_IntersectAOut.gff3"/>
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36 <output name="ob" file="T7_IntersectBOut.gff3"/>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40 **What it does**
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41
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42 Given two input files, this tool computes the members of A that are within
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43 "Window" nucleotides of a member of B, and vice versa. It then produces
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44 two gff3 outputs, one being the features of GFF A that pass this check,
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45 and the other being the features of GFF B that pass.
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46 ]]></help>
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47 <expand macro="citations-2020"/>
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48 </tool>