annotate protein_blast_grouping.xml @ 3:c5e0e05ce58a draft

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date Thu, 08 Aug 2024 03:33:45 +0000
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1 <tool id="edu.tamu.cpt.blast.protein_grouping" name="Protein Blast Grouping" version="0.0.1">
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2 <description>Based on a BLASTp result</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 <command detect_errors="aggressive">
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8 <![CDATA[
2
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9 python $__tool_directory__/protein_blast_grouping.py
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10 '${blast_in.blast}'
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11 --hits '$hits'
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12 --sort '$sort.sortType'
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13 --output '$grouping_output'
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14 ]]>
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15 </command>
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16 <inputs>
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17 <conditional name="blast_in">
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18 <param name="blastType" type="select" label="Blastn Input Type">
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19 <option value="TSV">Blast Tabular</option>
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20 </param>
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21 <when value="TSV">
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22 <param label="BLASTp Results" name="blast" type="data" format="tsv,tabular"/>
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23 </when>
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24 </conditional>
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25 <param label="Number of results to return" name="hits" type="integer" value="5" min="1" max="30"/>
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26 <conditional name="sort">
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27 <param name="sortType" type="select" label="Sort by">
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28 <option value="unique_queries" selected="true">Unique Queries</option>
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29 <option value="unique_hits">Unique Hits</option>
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30 </param>
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31 <when value="unique_queries"/>
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32 <when value="unique_hits"/>
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33 </conditional>
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34 </inputs>
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35 <outputs>
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36 <data format="tabular" name="grouping_output" label="Top BlastP Hits"/>
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37 </outputs>
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38 <tests>
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39 <test>
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40 <conditional name="blast_in">
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41 <param name="blastType" value="TSV"/>
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42 <param name="blast" value="infile.txt"/>
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43 </conditional>
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44 <param name="hits" value="20"/>
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45 <output name="grouping_output" file="outfile.txt" lines_diff="1"/>
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46 </test>
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47 </tests>
1
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48 <help><![CDATA[
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49 **What it does**
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50 * Reads a tab-delimited BLAST output file.
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51 * Extracts organism names from the subject titles (text in square brackets).
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52 * Counts unique query proteins that matched each organism and unique hit proteins from each organism.
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53 * Sorts and displays results based on either unique queries or unique hits.
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54 * The output is a formatted table showing the top N organisms with the most matches.
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55 ]]>
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56 </help>
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57 <expand macro="citations-2020"/>
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58 </tool>