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4
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1 <tool id="chewbbaca_createschema" name="chewBBACA CreateSchema" version="2.1.0+galaxy0">
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8
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2 <description>Create a gene by gene schema based on genomes</description>
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0
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3 <requirements>
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4
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4 <requirement type="package" version="2.1.0">chewbbaca</requirement>
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0
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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2
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7 chewBBACA.py CreateSchema
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0
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8 --cpu \${GALAXY_SLOTS:-1}
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11
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9 -i
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10 #for $assembly in $assemblies:
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11 $assembly
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12 #end for
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8
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13 #if str( $prodigal_training_file_source.prodigal_training_file_source_selector ) == 'tool_data_table':
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2
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14 --ptf '${prodigal_training_file_source.prodigal_training_file.fields.path}'
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8
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15 #elif str( $prodigal_training_file_source.prodigal_training_file_source_selector ) == 'history':
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2
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16 --ptf '${prodigal_training_file_source.prodigal_training_file}'
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17 #end if
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9
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18 #if $cds:
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2
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19 --CDS '${cds}'
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0
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20 #end if
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21 --bsr '${bsr}'
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22 -o schema
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23 && tar -czf schema.tgz schema
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24 ]]>
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25 </command>
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26 <inputs>
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2
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27 <param name="assemblies" format="fasta" type="data" multiple="true" label="Assembled genomes (fasta)" />
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5
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28 <conditional name="prodigal_training_file_source">
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2
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29 <param name="prodigal_training_file_source_selector" type="select"
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30 label="Select a Prodigal training file from your history or use one from a tool data table?">
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31 <option value="No" selected="true">No Prodigal training file</option>
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32 <option value="tool_data_table">Prodigal training file from tool data table</option>
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33 <option value="history">Prodigal training file from history</option>
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34 </param>
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35 <when value="No"/>
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36 <when value="tool_data_table">
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37 <param name="prodigal_training_file" type="select" format="tabular" label="Prodigal Training File">
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38 <options from_data_table="chewbbaca_prodigal_training_files">
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39 <validator type="no_options" message="No chewBBACA prodigal training files are available" />
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40 </options>
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41 </param>
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42 </when>
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43 <when value="history">
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44 <param name="prodigal_training_file" type="data" format="binary"
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45 label="Prodigal training file"
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46 help=""/>
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47 </when>
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48 </conditional>
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0
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49 <param name="bsr" type="float" value="0.6" optional="true" label="BSR score" />
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2
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50 <param name="cds" type="data" format="fasta" optional="true" label="Coding sequence file for schema creation (fasta)" />
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0
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51 </inputs>
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52 <outputs>
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53 <data name="schema_zipped" format="zip" label="${tool.name}: on ${on_string}: Schema (zipped)" from_work_dir="schema.tgz"/>
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54 </outputs>
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55 <tests>
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56
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57 </tests>
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58 <help><![CDATA[
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59 ]]>
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60 </help>
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61 <expand macro="citations"/>
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62 </tool>
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