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1 <tool id="edu.tamu.cpt2.phage.disruptin_finder" name="Disruptin Finder" version="1.1">
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2 <description>finds proteins with size and charge criteria</description>
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3 <macros>
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4 <import>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 python '$__tool_directory__/disruptin_finder.py'
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10 '$fasta_file'
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11 --thresh_net_charge '$thresh_net_charge'
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12 --thresh_size '$thresh_size'
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13 --thresh_charge_ratio '$thresh_charge_ratio'
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14 --selection_criteria '$selection_criteria'
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16 > '$output']]></command>
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17 <inputs>
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18 <param label="Fasta" name="fasta_file" type="data" format="fasta"/>
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19 <param label="Minimum Net Charge" name="thresh_net_charge" type="integer" value="4"/>
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20 <param label="Maximum Length" name="thresh_size" type="integer" value="100"/>
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21 <param label="Minimum Charge to Length Ratio" name="thresh_charge_ratio" type="float" value="0.25"/>
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22 <param type="select" label="Type of selection criteria" name="selection_criteria">
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23 <option value="net">Net charge</option>
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24 <option value="ratio">Ratio of charged residues to sequence length</option>
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25 <option value="both" selected="true">Both net charge and ratio</option>
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26 </param>
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27 </inputs>
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28 <outputs>
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29 <data format="fasta" name="output"/>
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30 </outputs>
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31 <help><![CDATA[
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32 **What it does**
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33 This program finds proteins sequences based on given selection criteria: net charge, sequence length,
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34 and/or number of charged residues per amino acid. Inputs include a multi fasta file of protein sequences,
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35 thresholds for size, charge, and charge-to-size ratio criteria.
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36
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37 This tool returns the selected sequences in a fasta format.
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38
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39 ]]></help>
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40 <citations>
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41 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
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42 <citation type="bibtex">
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43 @unpublished{galaxyTools,
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44 author = {A. Holt},
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45 title = {CPT Galaxy Tools},
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46 year = {2020},
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47 note = {https://github.com/tamu-cpt/galaxy-tools/}
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48 }
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49 </citation>
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50 </citations>
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51 </tool>