Mercurial > repos > dfornika > chewbbaca_createschema
annotate chewbbaca_createschema.xml @ 16:badf5248b6c2 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 071e014d347109e5c18cc50595498d3d43ef0323-dirty"
| author | dfornika |
|---|---|
| date | Tue, 02 Jun 2020 20:34:37 +0000 |
| parents | 1b0a69b7b2c9 |
| children |
| rev | line source |
|---|---|
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1b0a69b7b2c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 90d84ed39bfd0d34e10cec9f417953042404648a-dirty"
dfornika
parents:
13
diff
changeset
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1 <tool id="chewbbaca_createschema" name="chewBBACA CreateSchema" version="@TOOL_VERSION@+galaxy0"> |
| 8 | 2 <description>Create a gene by gene schema based on genomes</description> |
| 0 | 3 <requirements> |
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1b0a69b7b2c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 90d84ed39bfd0d34e10cec9f417953042404648a-dirty"
dfornika
parents:
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diff
changeset
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4 <requirement type="package" version="@TOOL_VERSION@">chewbbaca</requirement> |
| 0 | 5 </requirements> |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 12 | 7 mkdir assemblies && |
| 13 | 8 ln -s |
| 12 | 9 #for $assembly in $assemblies: |
| 13 | 10 '${assembly}' |
| 12 | 11 #end for |
| 13 | 12 assemblies && |
| 2 | 13 chewBBACA.py CreateSchema |
| 0 | 14 --cpu \${GALAXY_SLOTS:-1} |
| 12 | 15 -i assemblies |
| 8 | 16 #if str( $prodigal_training_file_source.prodigal_training_file_source_selector ) == 'tool_data_table': |
| 2 | 17 --ptf '${prodigal_training_file_source.prodigal_training_file.fields.path}' |
| 8 | 18 #elif str( $prodigal_training_file_source.prodigal_training_file_source_selector ) == 'history': |
| 2 | 19 --ptf '${prodigal_training_file_source.prodigal_training_file}' |
| 20 #end if | |
| 9 | 21 #if $cds: |
| 2 | 22 --CDS '${cds}' |
| 0 | 23 #end if |
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1b0a69b7b2c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 90d84ed39bfd0d34e10cec9f417953042404648a-dirty"
dfornika
parents:
13
diff
changeset
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24 --bsr '${min_bsr}' |
| 0 | 25 -o schema |
| 26 && tar -czf schema.tgz schema | |
| 27 ]]> | |
| 28 </command> | |
| 29 <inputs> | |
| 13 | 30 <param name="assemblies" format="fasta" type="data_collection" collection_type="list" label="Assembled genomes (fasta)" /> |
| 5 | 31 <conditional name="prodigal_training_file_source"> |
| 2 | 32 <param name="prodigal_training_file_source_selector" type="select" |
| 33 label="Select a Prodigal training file from your history or use one from a tool data table?"> | |
| 34 <option value="No" selected="true">No Prodigal training file</option> | |
| 35 <option value="tool_data_table">Prodigal training file from tool data table</option> | |
| 36 <option value="history">Prodigal training file from history</option> | |
| 37 </param> | |
| 38 <when value="No"/> | |
| 39 <when value="tool_data_table"> | |
| 40 <param name="prodigal_training_file" type="select" format="tabular" label="Prodigal Training File"> | |
| 13 | 41 <options from_data_table="prodigal_training_files"> |
| 42 <validator type="no_options" message="No prodigal training files are available" /> | |
| 2 | 43 </options> |
| 44 </param> | |
| 45 </when> | |
| 46 <when value="history"> | |
| 47 <param name="prodigal_training_file" type="data" format="binary" | |
| 48 label="Prodigal training file" | |
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1b0a69b7b2c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 90d84ed39bfd0d34e10cec9f417953042404648a-dirty"
dfornika
parents:
13
diff
changeset
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49 help="Prodigal training file"/> |
| 2 | 50 </when> |
| 51 </conditional> | |
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15
1b0a69b7b2c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 90d84ed39bfd0d34e10cec9f417953042404648a-dirty"
dfornika
parents:
13
diff
changeset
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52 <param name="min_bsr" type="float" value="0.6" optional="true" label="Minimum BLAST Score Ratio (BSR) Similarity" /> |
| 2 | 53 <param name="cds" type="data" format="fasta" optional="true" label="Coding sequence file for schema creation (fasta)" /> |
| 0 | 54 </inputs> |
| 55 <outputs> | |
| 13 | 56 <data name="schema" type="list" format="fasta" label="${tool.name}: on ${on_string}: Schema"> |
| 57 <discover_datasets pattern="__name_and_ext__" format="fasta" directory="schema" /> | |
| 58 </data> | |
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16
badf5248b6c2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 071e014d347109e5c18cc50595498d3d43ef0323-dirty"
dfornika
parents:
15
diff
changeset
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59 <data name="schema_zipped" format="zip" label="${tool.name}: on ${on_string}: Schema (zipped)" from_work_dir="schema.tgz"> |
| 13 | 60 </data> |
| 0 | 61 </outputs> |
| 62 <tests> | |
| 13 | 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> | |
| 0 | 85 </tests> |
| 86 <help><![CDATA[ | |
| 87 ]]> | |
| 88 </help> | |
| 89 <expand macro="citations"/> | |
| 90 </tool> |