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1 <?xml version="1.0"?>
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2 <tool id="edu.tamu.cpt.gff.stop_codons" name="Stop Codon Statistics" version="1.0">
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3 <description>Summarise stop codon usage</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <import>cpt-macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="aggressive"><![CDATA[
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10 @GENOME_SELECTOR_PRE@
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11
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12 $__tool_directory__/stop_stats.py
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13
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14 @GENOME_SELECTOR@
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15 $gff3_data
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16 > $default]]></command>
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17 <inputs>
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18 <expand macro="genome_selector" />
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19 <expand macro="gff3_input" />
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20 </inputs>
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21 <outputs>
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22 <data format="tabular" name="default" label="Stop Codon Usage"/>
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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="reference_genome_source" value="history" />
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27 <param name="genome_fasta" value="miro.fa" />
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28 <param name="gff3_data" value="miro.gff3" />
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29
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30 <output name="default" value="stop-stats.tab" />
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31 </test>
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32 </tests>
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33 <help><![CDATA[
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34 .. class:: warningmark
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35
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36 This tool is deprecated. Please use `the new fasta-only tool <root?tool_id=edu.tamu.cpt.fasta.stop_codons>`__.
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37 This change was made to make the tools less complicated and more obvious in
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38 their functionality. Currently this tool makes **assumptions** about your data
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39 which **may be wrong**.
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40
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41 **What it does**
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42
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43 This tool looks for CDS features and outputs summarizes the frequencies
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44 of their stop codons::
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45
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46
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47 # Name Codon Count
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48 Ochre TAA 155
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49 Amber TAG 10
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50 Opal TGA 111
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51 ]]></help>
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52 <expand macro="citations" />
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53 </tool>
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