Mercurial > repos > dfornika > chewbbaca_createschema
comparison chewbbaca_createschema.xml @ 2:fed8439686cb draft
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author | dfornika |
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date | Fri, 21 Feb 2020 01:14:47 +0000 |
parents | 470f58372a68 |
children | 75d3a1fb5f5a |
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1:8bcac51c233c | 2:fed8439686cb |
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1 <tool id="chewbbaca_prepexternalschema" name="chewBBACA PrepExternalSchema" version="@TOOL_VERSION@+galaxy0"> | 1 <tool id="chewbbaca_createschema" name="chewBBACA CreateSchema" version="@TOOL_VERSION@+galaxy0"> |
2 <description>Adapt an external schema to be used with chewBBACA.</description> | 2 <description>Adapt an external schema to be used with chewBBACA.</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="@TOOL_VERSION@">chewbbaca</requirement> | 4 <requirement type="package" version="@TOOL_VERSION@">chewbbaca</requirement> |
5 </requirements> | 5 </requirements> |
6 <command detect_errors="exit_code"><![CDATA[ | 6 <command detect_errors="exit_code"><![CDATA[ |
7 chewBBACA.py PrepExternalSchema | 7 chewBBACA.py CreateSchema |
8 --cpu \${GALAXY_SLOTS:-1} | 8 --cpu \${GALAXY_SLOTS:-1} |
9 -i '${input_files}' | 9 -i '${assemblies}' |
10 #if str( translation_table ) != "": | 10 #if str( prodigal_training_file_source.prodigal_training_file_source_selector ) == 'tool_data_table' |
11 --tbl '${translation_table}' | 11 --ptf '${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}' | |
12 #end if | 17 #end if |
13 --bsr '${bsr}' | 18 --bsr '${bsr}' |
14 --len '${len}' | 19 --len '${len}' |
15 -o schema | 20 -o schema |
16 && tar -czf schema.tgz schema | 21 && tar -czf schema.tgz schema |
17 ]]> | 22 ]]> |
18 </command> | 23 </command> |
19 <inputs> | 24 <inputs> |
20 <param name="input_files" format="fasta" type="data" multiple="true" label="Schema files (fasta)" /> | 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> | |
21 <param name="bsr" type="float" value="0.6" optional="true" label="BSR score" /> | 47 <param name="bsr" type="float" value="0.6" optional="true" label="BSR score" /> |
22 <param name="min_len" type="integer" min="1" value="100" max="100000" optional="true" label="Minimum length" /> | 48 <param name="cds" type="data" format="fasta" optional="true" label="Coding sequence file for schema creation (fasta)" /> |
23 </inputs> | 49 </inputs> |
24 <outputs> | 50 <outputs> |
25 <data name="schema_zipped" format="zip" label="${tool.name}: on ${on_string}: Schema (zipped)" from_work_dir="schema.tgz"/> | 51 <data name="schema_zipped" format="zip" label="${tool.name}: on ${on_string}: Schema (zipped)" from_work_dir="schema.tgz"/> |
26 </outputs> | 52 </outputs> |
27 <tests> | 53 <tests> |