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annotate disruptin_proximity_2_lysis_genes.xml @ 1:5081ba961953 draft

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author cpt
date Mon, 05 Jun 2023 02:40:58 +0000
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1 <tool id="edu.tamu.cpt2.phage.disruptin_prox" name="Disruptin Proximity to Lysis Genes Tool" version="1.1">
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2 <description>identifies lysis gene candidates close to genes encoding endolysin domains and genes encoding transmembrane domains</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="3.0.2">intervaltree</requirement>
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9 </expand>
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10 <command detect_errors="aggressive"><![CDATA[
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11 python '$__tool_directory__/disruptin_proximity_2_lysis_genes.py'
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12 '$lgc'
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13 '$tmhmm'
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14 '$ipro'
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15 '$genome'
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16 '$window'
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17 '$enzyme'
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18 --oa '$oa'
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19 --ob '$ob'
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20 --oc '$oc'
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21 --od '$od'
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22
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23 ]]></command>
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24 <inputs>
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25 <param label="Lysis Gene Candidates" name="lgc" type="data" format="fasta"/>
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26 <param label="TMHMM Results" name="tmhmm" type="data" format="gff3"/>
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27 <param label="InterProScan Results" name="ipro" type="data" format="gff3"/>
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28 <param label="Phage Genome" name="genome" type="data" format="gff3"/>
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29 <param label="Adjacency Window Size" name="window" type="integer" value="1000"/>
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30 <param label="Enzyme Domain List" name="enzyme" type="data" format="tabular"/>
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31 </inputs>
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32 <outputs>
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33 <data format="gff3" name="oa" label="Protein with endolysin-associated domain and adjacent to lysis gene candidate"/>
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34 <data format="gff3" name="ob" label="Lysis gene candidates near possible endolysin"/>
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35 <data format="gff3" name="oc" label="Protein with transmembrane domain and adjacent to lysis gene candidate"/>
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36 <data format="gff3" name="od" label="Lysis gene candidates near TMD-containing protein"/>
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37 </outputs>
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38 <help><![CDATA[
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39 **What it does**
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40 This program is intended to identify protein coding sequences within a certain window (number of base pairs) of genes encoding recognized endolysin domains and others encoding transmembrane domains.
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41 The goal is to identify possible lysis genes or to narrow a list of disruptin candidates.
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42
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43 ]]></help>
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44 <citations>
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45 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
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46 <citation type="bibtex">
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47 @unpublished{galaxyTools,
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48 author = {A. Holt},
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49 title = {CPT Galaxy Tools},
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50 year = {2020},
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51 note = {https://github.com/tamu-cpt/galaxy-tools/}
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52 }
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53 </citation>
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54 </citations>
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55 </tool>