Mercurial > repos > dfornika > chewbbaca_createschema
comparison chewbbaca_createschema.xml @ 13:35ee71a46436 draft
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author | dfornika |
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date | Fri, 21 Feb 2020 23:28:08 +0000 |
parents | 64a7d9e95445 |
children | 1b0a69b7b2c9 |
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12:64a7d9e95445 | 13:35ee71a46436 |
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3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="2.1.0">chewbbaca</requirement> | 4 <requirement type="package" version="2.1.0">chewbbaca</requirement> |
5 </requirements> | 5 </requirements> |
6 <command detect_errors="exit_code"><![CDATA[ | 6 <command detect_errors="exit_code"><![CDATA[ |
7 mkdir assemblies && | 7 mkdir assemblies && |
8 ln -s | |
8 #for $assembly in $assemblies: | 9 #for $assembly in $assemblies: |
9 ln -s $assembly assemblies && | 10 '${assembly}' |
10 #end for | 11 #end for |
12 assemblies && | |
11 chewBBACA.py CreateSchema | 13 chewBBACA.py CreateSchema |
12 --cpu \${GALAXY_SLOTS:-1} | 14 --cpu \${GALAXY_SLOTS:-1} |
13 -i assemblies | 15 -i assemblies |
14 #if str( $prodigal_training_file_source.prodigal_training_file_source_selector ) == 'tool_data_table': | 16 #if str( $prodigal_training_file_source.prodigal_training_file_source_selector ) == 'tool_data_table': |
15 --ptf '${prodigal_training_file_source.prodigal_training_file.fields.path}' | 17 --ptf '${prodigal_training_file_source.prodigal_training_file.fields.path}' |
23 -o schema | 25 -o schema |
24 && tar -czf schema.tgz schema | 26 && tar -czf schema.tgz schema |
25 ]]> | 27 ]]> |
26 </command> | 28 </command> |
27 <inputs> | 29 <inputs> |
28 <param name="assemblies" format="fasta" type="data" multiple="true" label="Assembled genomes (fasta)" /> | 30 <param name="assemblies" format="fasta" type="data_collection" collection_type="list" label="Assembled genomes (fasta)" /> |
29 <conditional name="prodigal_training_file_source"> | 31 <conditional name="prodigal_training_file_source"> |
30 <param name="prodigal_training_file_source_selector" type="select" | 32 <param name="prodigal_training_file_source_selector" type="select" |
31 label="Select a Prodigal training file from your history or use one from a tool data table?"> | 33 label="Select a Prodigal training file from your history or use one from a tool data table?"> |
32 <option value="No" selected="true">No Prodigal training file</option> | 34 <option value="No" selected="true">No Prodigal training file</option> |
33 <option value="tool_data_table">Prodigal training file from tool data table</option> | 35 <option value="tool_data_table">Prodigal training file from tool data table</option> |
34 <option value="history">Prodigal training file from history</option> | 36 <option value="history">Prodigal training file from history</option> |
35 </param> | 37 </param> |
36 <when value="No"/> | 38 <when value="No"/> |
37 <when value="tool_data_table"> | 39 <when value="tool_data_table"> |
38 <param name="prodigal_training_file" type="select" format="tabular" label="Prodigal Training File"> | 40 <param name="prodigal_training_file" type="select" format="tabular" label="Prodigal Training File"> |
39 <options from_data_table="chewbbaca_prodigal_training_files"> | 41 <options from_data_table="prodigal_training_files"> |
40 <validator type="no_options" message="No chewBBACA prodigal training files are available" /> | 42 <validator type="no_options" message="No prodigal training files are available" /> |
41 </options> | 43 </options> |
42 </param> | 44 </param> |
43 </when> | 45 </when> |
44 <when value="history"> | 46 <when value="history"> |
45 <param name="prodigal_training_file" type="data" format="binary" | 47 <param name="prodigal_training_file" type="data" format="binary" |
49 </conditional> | 51 </conditional> |
50 <param name="bsr" type="float" value="0.6" optional="true" label="BSR score" /> | 52 <param name="bsr" type="float" value="0.6" optional="true" label="BSR score" /> |
51 <param name="cds" type="data" format="fasta" optional="true" label="Coding sequence file for schema creation (fasta)" /> | 53 <param name="cds" type="data" format="fasta" optional="true" label="Coding sequence file for schema creation (fasta)" /> |
52 </inputs> | 54 </inputs> |
53 <outputs> | 55 <outputs> |
54 <data name="schema_zipped" format="zip" label="${tool.name}: on ${on_string}: Schema (zipped)" from_work_dir="schema.tgz"/> | 56 <data name="schema" type="list" format="fasta" label="${tool.name}: on ${on_string}: Schema"> |
57 <discover_datasets pattern="__name_and_ext__" format="fasta" directory="schema" /> | |
58 </data> | |
59 <data name="schema_zipped" format="zip" label="${tool.name}: on ${on_string}: Schema (zipped)" from_work_dir="schema.tgz"> | |
60 </data> | |
55 </outputs> | 61 </outputs> |
56 <tests> | 62 <tests> |
57 | 63 <test> |
64 <param name="prodigal_training_file_source_selector" value="history" /> | |
65 <param name="prodigal_training_file" value="prodigal_training_files/Streptococcus_agalactiae.trn" /> | |
66 <param name="assemblies"> | |
67 <collection type="list"> | |
68 <element name="assembly1" value="assemblies/GCA_000007265.1_ASM726v1_genomic_2kbases.fna" /> | |
69 <element name="assembly2" value="assemblies/GCA_000012705.1_ASM1270v1_genomic_2kbases.fna" /> | |
70 </collection> | |
71 </param> | |
72 <output name="schema_zipped" file="test_1_schema.tgz" compare="sim_size" /> | |
73 </test> | |
74 <test> | |
75 <param name="prodigal_training_file_source_selector" value="tool_data_table" /> | |
76 <param name="prodigal_training_file" value="Streptococcus_agalactiae" /> | |
77 <param name="assemblies"> | |
78 <collection type="list"> | |
79 <element name="assembly1" value="assemblies/GCA_000007265.1_ASM726v1_genomic_2kbases.fna" /> | |
80 <element name="assembly2" value="assemblies/GCA_000012705.1_ASM1270v1_genomic_2kbases.fna" /> | |
81 </collection> | |
82 </param> | |
83 <output name="schema_zipped" file="test_1_schema.tgz" compare="sim_size" /> | |
84 </test> | |
58 </tests> | 85 </tests> |
59 <help><![CDATA[ | 86 <help><![CDATA[ |
60 ]]> | 87 ]]> |
61 </help> | 88 </help> |
62 <expand macro="citations"/> | 89 <expand macro="citations"/> |