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annotate intersect_and_adjacent.xml @ 1:f7d19040fafa draft
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date | Sun, 11 Aug 2024 22:22:44 +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 <requirements> |
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8 <requirement type="package" version="3.0.2">intervaltree</requirement> |
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9 </requirements> |
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10 <command detect_errors="aggressive"><![CDATA[ |
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11 python '$__tool_directory__/intersect_and_adjacent.py' |
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12 '$gff3_data_a' |
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13 '$gff3_data_b' |
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14 '$window' |
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15 '$stranding' |
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16 --oa '$oa' |
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17 --ob '$ob' |
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18 ]]> |
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19 </command> |
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20 <inputs> |
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21 <param label="GFF3 Annotations A" name="gff3_data_a" type="data" format="gff3"/> |
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22 <param label="GFF3 Annotations B" name="gff3_data_b" type="data" format="gff3"/> |
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23 <param label="Adjacency Window Size" name="window" type="integer" value="0"/> |
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24 <param label="Only allow adjacencies for features on the same strand" name="stranding" type="boolean" checked="false" truevalue="-stranding" falsevalue=""/> |
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25 </inputs> |
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26 <outputs> |
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27 <data format="gff3" name="oa" label="GFF3 Annotations from ${gff3_data_a.name} in ${gff3_data_b.name}"/> |
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28 <data format="gff3" name="ob" label="GFF3 Annotations from ${gff3_data_b.name} in ${gff3_data_a.name}"/> |
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29 </outputs> |
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30 <tests> |
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31 <test> |
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32 <param name="gff3_data_a" value="T7_IntersectAIn.gff3"/> |
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33 <param name="gff3_data_b" value="T7_IntersectBIn.gff3"/> |
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34 <param name="window" value="50"/> |
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35 <param name="stranding" value="-stranding"/> |
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36 <output name="oa" file="T7_IntersectAOut.gff3"/> |
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37 <output name="ob" file="T7_IntersectBOut.gff3"/> |
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38 </test> |
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39 </tests> |
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40 <help><![CDATA[ |
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41 **What it does** |
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42 |
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43 Given two input files, this tool computes the members of A that are within |
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44 "Window" nucleotides of a member of B, and vice versa. It then produces |
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45 two gff3 outputs, one being the features of GFF A that pass this check, |
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46 and the other being the features of GFF B that pass. |
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47 ]]></help> |
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48 <expand macro="citations-2020"/> |
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49 </tool> |