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