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annotate data_manager/ariba_database_builder.xml @ 3:b13f7ba85697 draft

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Update ariba_database_builder.py
author thanhlv
date Mon, 14 Jan 2019 07:01:15 -0500
parents 204f94dc1c2c
children be46816110b4
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1 <?xml version="1.0"?>
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2 <tool id="ariba_database_builder" name="ARIBA build database" tool_type="manage_data" version="@VERSION@">
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3 <description>Download and prepare database for use with ARIBA</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <version_command>ariba version | head head -n 1</version_command>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 #if str($library.lib_type) == "curated"
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12 #set $library_list = str($library.curated).split(',')
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13 #for $library_ in $library_list:
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14 #if str($library_) != 'None':
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15 ariba getref '$library_' _tmp_db && ariba prepareref -f _tmp_db.fa -m _tmp_db.tsv '$library_' &&
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16 #end if
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17 #end for
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18 #end if
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19
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20 #if str($library.lib_type) == "fasta"
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21 #if str($library).fasta != 'None':
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22 ariba prepareref --all_coding '$coding' -f '$library.fasta' '$library.db_name'
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23 #end if
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24 #end if
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25
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26 python '$__tool_directory__/ariba_database_builder.py' --out '${out_file}'
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27 ]]>
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28 </command>
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29 <inputs>
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30 <conditional name="library">
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31 <param name="lib_type" type="select" label="Input reads type or collection" help="Select a curated database or a fasta from the history">
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32 <option value="curated" selected="true">Curated Database</option>
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33 <option value="fasta">A fasta file</option>
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34 </param>
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35 <when value="curated">
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36 <param name="curated" type="select" multiple="true" label="Select partial library to download">
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37 <option value="card">CARD</option>
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38 <option value="resfinder">Resfinder</option>
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39 <option value="plasmidfinder">Plasmidfinder</option>
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40 <option value="megares">Megares</option>
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41 <option value="argannot">Argannot</option>
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42 <option value="vfdb_core">vfdb_core</option>
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43 <option value="vfdb_full">vfdb_full</option>
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44 <option value="virulencefinder">virulencefinder</option>
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45 </param>
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46 </when>
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47 <when value="fasta">
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48 <param name="fasta" type="data" format="fasta" optional="false" />
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49 <param name="db_name" type="text" label="DB name" help = "The DB name should include no space and special characters" />
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50 <param name="coding" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="Coding sequence?" />
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51 </when>
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52 </conditional>
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53 </inputs>
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54 <outputs>
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55 <data name="out_file" format="data_manager_json" />
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56 </outputs>
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57 <help>
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58 </help>
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59 <citations>
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60 <citation type="doi">110.1099/mgen.0.000131</citation>
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61 </citations>
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62 </tool>