Mercurial > repos > cpt > cpt_blasttab_dice_filter
annotate blasttab_dice_filter.xml @ 5:99baf3ee2a2b draft
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author | cpt |
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date | Mon, 05 Jun 2023 02:40:11 +0000 |
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children | f6d253d91757 |
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1 <tool id="edu.tamu.cpt.blast.blasttab_dice_filter" name="Blast Tabular Dice Filter" version="19.1.0.0"> |
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2 <description>removes low-dice blast results</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 '$__tool_directory__/blasttab_dice_filter.py' |
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10 @BLAST_TSV@ |
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11 --min_dice '$min_dice' |
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12 > '$output']]></command> |
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13 <inputs> |
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14 <expand macro="blast_tsv"/> |
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15 <param label="Minimum dice score" help="Blast results with a dice score below this value will be removed" name="min_dice" type="float" value="0.5" min="0.0" max="1.0"/> |
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16 </inputs> |
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17 <outputs> |
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18 <data format="tabular" name="output"/> |
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19 </outputs> |
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20 <tests> |
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21 <test> |
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22 <param name="blast_tsv" value="T7_NT_BLAST.tabular"/> |
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23 <param name="min_dice" value="0.2"/> |
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24 <output name="output" file="T7_NT_BLAST_FILTERED.tabular"/> |
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25 </test> |
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26 <test> |
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27 <param name="blast_tsv" value="results.tsv"/> |
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28 <param name="min_dice" value="0.5"/> |
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29 <output name="output" file="results.diced.tsv"/> |
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30 </test> |
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31 </tests> |
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32 <help><![CDATA[ |
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33 **What it does** |
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34 |
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35 Filters your tabular BLAST results based on a dice score thresholding process. |
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36 |
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37 **How it works** |
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38 |
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39 The tool processes BLAST results line by line, at each line calculating the dice score. |
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40 The equation for the dice score is as follows:: |
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41 |
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42 2 * number of identical matches / (query sequence length + subject sequence length) |
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43 |
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44 The denominator normalizes the score by accounting for the length of both sequences. A |
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45 pairwise alignment is required to have between 50-100% identity. |
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46 |
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47 ]]></help> |
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48 <expand macro="citations"/> |
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49 </tool> |