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1 <tool id="TransTermHP" name="TransTermHP" version="19.1.0.0">
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2 <description>predicts transcription terminators</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 <requirements>
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8 <requirement type="package" version="3.7.9">python</requirement>
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9 <requirement type="package" version="1.77">biopython</requirement>
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10 <requirement type="package" version="2.09">transtermhp</requirement>
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11 <requirement type="package" version="1.1.3">cpt_gffparser</requirement>
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12 <requirement type="package" version="1.5">bcftools</requirement>
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13 </requirements>
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14 <command detect_errors="aggressive"><![CDATA[
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15 @GENOME_SELECTOR_PRE@
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16
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17 $__tool_directory__/transterm.py
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18 @GENOME_SELECTOR@
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19 $gff3_data
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20
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21 > $output
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22
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23 ]]>
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24 </command>
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25 <inputs>
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26 <expand macro="genome_selector" />
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27 <expand macro="gff3_input" />
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28 </inputs>
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29 <outputs>
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30 <data name="output" label="Terminators from ${gff3_data.name}" format="gff3" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="genome_fasta" value="Transterm_In.fa" />
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35 <param name="gff3_data" value="Transterm_In.gff3" />
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36 <output name="output" file="Transterm_Out.gff3" />
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37 </test>
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38 </tests>
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39 <help>
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40 *TransTermHP* finds rho-independent transcription terminators in bacterial
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41 genomes. Each terminator found by the program is assigned a confidence
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42 value that estimates its probability of being a true terminator.
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43 </help>
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44 <citations>
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45 <citation type="doi">10.1186/gb-2007-8-2-r22</citation>
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46 </citations>
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47 </tool>
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