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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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12
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7 mkdir assemblies &&
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13
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8 ln -s
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12
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9 #for $assembly in $assemblies:
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13
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10 '${assembly}'
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12
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11 #end for
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13
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12 assemblies &&
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2
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13 chewBBACA.py CreateSchema
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0
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14 --cpu \${GALAXY_SLOTS:-1}
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12
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15 -i assemblies
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8
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16 #if str( $prodigal_training_file_source.prodigal_training_file_source_selector ) == 'tool_data_table':
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2
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17 --ptf '${prodigal_training_file_source.prodigal_training_file.fields.path}'
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8
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18 #elif str( $prodigal_training_file_source.prodigal_training_file_source_selector ) == 'history':
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2
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19 --ptf '${prodigal_training_file_source.prodigal_training_file}'
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20 #end if
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9
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21 #if $cds:
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2
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22 --CDS '${cds}'
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0
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23 #end if
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24 --bsr '${bsr}'
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25 -o schema
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26 && tar -czf schema.tgz schema
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27 ]]>
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28 </command>
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29 <inputs>
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13
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30 <param name="assemblies" format="fasta" type="data_collection" collection_type="list" label="Assembled genomes (fasta)" />
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5
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31 <conditional name="prodigal_training_file_source">
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2
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32 <param name="prodigal_training_file_source_selector" type="select"
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33 label="Select a Prodigal training file from your history or use one from a tool data table?">
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34 <option value="No" selected="true">No Prodigal training file</option>
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35 <option value="tool_data_table">Prodigal training file from tool data table</option>
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36 <option value="history">Prodigal training file from history</option>
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37 </param>
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38 <when value="No"/>
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39 <when value="tool_data_table">
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40 <param name="prodigal_training_file" type="select" format="tabular" label="Prodigal Training File">
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13
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41 <options from_data_table="prodigal_training_files">
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42 <validator type="no_options" message="No prodigal training files are available" />
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2
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43 </options>
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44 </param>
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45 </when>
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46 <when value="history">
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47 <param name="prodigal_training_file" type="data" format="binary"
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48 label="Prodigal training file"
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49 help=""/>
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50 </when>
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51 </conditional>
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0
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52 <param name="bsr" type="float" value="0.6" optional="true" label="BSR score" />
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2
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53 <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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54 </inputs>
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55 <outputs>
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13
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56 <data name="schema" type="list" format="fasta" label="${tool.name}: on ${on_string}: Schema">
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57 <discover_datasets pattern="__name_and_ext__" format="fasta" directory="schema" />
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58 </data>
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59 <data name="schema_zipped" format="zip" label="${tool.name}: on ${on_string}: Schema (zipped)" from_work_dir="schema.tgz">
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60 </data>
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0
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61 </outputs>
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62 <tests>
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13
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63 <test>
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64 <param name="prodigal_training_file_source_selector" value="history" />
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65 <param name="prodigal_training_file" value="prodigal_training_files/Streptococcus_agalactiae.trn" />
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66 <param name="assemblies">
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67 <collection type="list">
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68 <element name="assembly1" value="assemblies/GCA_000007265.1_ASM726v1_genomic_2kbases.fna" />
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69 <element name="assembly2" value="assemblies/GCA_000012705.1_ASM1270v1_genomic_2kbases.fna" />
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70 </collection>
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71 </param>
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72 <output name="schema_zipped" file="test_1_schema.tgz" compare="sim_size" />
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73 </test>
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74 <test>
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75 <param name="prodigal_training_file_source_selector" value="tool_data_table" />
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76 <param name="prodigal_training_file" value="Streptococcus_agalactiae" />
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77 <param name="assemblies">
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78 <collection type="list">
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79 <element name="assembly1" value="assemblies/GCA_000007265.1_ASM726v1_genomic_2kbases.fna" />
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80 <element name="assembly2" value="assemblies/GCA_000012705.1_ASM1270v1_genomic_2kbases.fna" />
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81 </collection>
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82 </param>
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83 <output name="schema_zipped" file="test_1_schema.tgz" compare="sim_size" />
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84 </test>
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0
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85 </tests>
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86 <help><![CDATA[
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87 ]]>
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88 </help>
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89 <expand macro="citations"/>
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90 </tool>
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