Mercurial > repos > cpt > cpt_blast_to_xmfa

annotate blast2pxmfa.xml @ 1:c66d6978a5f8 draft

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author cpt
date Mon, 05 Jun 2023 02:14:17 +0000
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1 <tool id="edu.tamu.cpt.blast.blast2pxmfa" name="Blast TSV to Protein XMFA" version="1.0">
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2 <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 <requirement type="package" version="2.1">clustalw</requirement>
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9 </expand>
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10 <command detect_errors="aggressive"><![CDATA[
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11 '$__tool_directory__/blast2pxmfa.py'
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12 @BLAST_TSV@
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13 '$fasta'
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14 '$gff3'
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15 '$output'
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16 ]]></command>
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17 <inputs>
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18 <expand macro="blast_tsv"/>
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19 <expand macro="gff3_with_fasta"/>
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20 </inputs>
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21 <outputs>
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22 <data format="pxmfa" name="output"/>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="blast_tsv" value="results.tsv"/>
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27 <param name="fasta" value="related.fa"/>
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28 <param name="gff3" value="related.gbk.gff"/>
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29 <output name="output" file="cbk.xmfa">
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30 <assert_contents>
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31 <has_n_lines n="7547" delta="100"/>
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32 </assert_contents>
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33 </output>
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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37 .. class:: warningmark
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38
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39 You likely should first filter your data first using the `Blast Tabular Dice
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40 Filter tool <root?tool_id=edu.tamu.cpt.blast.blasttab_dice_filter>`__.
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41
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42 **What it does**
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43
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44 This tool processes BLAST Tabular results into a *protein* XMFA file. This
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45 permits visualizing the data with CPT developed XMFA based tooling.
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46
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47 **How it works**
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48
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49 The tool works by:
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50
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51 - taking the set of blast results
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52 - clustering them according to relationships detected by blast
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53 - running ClustalW to generate a set of alignments for each cluster
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54 - outputting those clusters in the XMFA format
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55 ]]></help>
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56 <citations>
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57 </citations>
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58 </tool>